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vcf2maf_cluster.tar
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vcf2maf_cluster.tar
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vcf2maf_cluster/ 0000775 0001750 0001750 00000000000 14434476554 014367 5 ustar lucianhu lucianhu vcf2maf_cluster/run_vcf2maf_cluster_2023.sh 0000664 0001750 0001750 00000013063 14434476422 021337 0 ustar lucianhu lucianhu #!/bin/bash
# Define the usage guide
usage() {
echo "NAME"
echo " run_vcf2maf_cluster_2023.sh - Execute the bash file and run the vcf2maf.pl script for the conversion of a VCF file to a MAF file."
echo ""
echo "SYNOPSIS"
echo " run_vcf2maf_cluster_2023.sh --help"
echo " run_vcf2maf_cluster_2023.sh --datadir \"/path/to/datadir\" --vcfdir \"/path/to/datadir/raw_vcf\" --vcf2mafdir \"/path/to/vcf2maf-1.6.21\" --ref_fasta \"/path/to/.vep/homo_sapiens/109_GRCh38/Homo_sapiens.GRCh39.dna.toplevel.fa.gz\" --vep_path \"/path/to/miniconda3/bin\" --vep_data \"/path/to/.vep\""
echo ""
echo "OPTIONS"
echo " --h, --help Shows this help message and exit"
echo " --datadir Folder containing both the input and output data."
echo " --vcfdir Path to input file in VCF format."
echo " --vcf2mafdir Folder containing the vcf2maf script."
# E.g: /home/ad.dkfz-heidelberg.de/q874n/softwares/vcf2maf-1.6.21
# E.g: $HOME/softwares/vcf2maf-1.6.21
echo " --ref_fasta Reference FASTA file."
# E.g: /home/ad.dkfz-heidelberg.de/q874n/softwares/vep96_GRCh37/homo_sapiens/96_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz
# E.g: $HOME/softwares/vep96_GRCh37/homo_sapiens/96_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz
echo " --vep_data VEP's base cache/plugin directory."
# E.g: $HOME/softwares/vep96_GRCh37
echo ""
}
# Check if no arguments are provided or --help is specified
if [[ $# -eq 0 ]] || [[ $1 == "--help" ]] || [[ $1 == "--h" ]]; then
usage
exit 0
fi
# Parse the command-line arguments
while [[ $# -gt 0 ]]; do # Check if the number of command-line arguments `$#` is greater than 0. `$#` is a special shell variable that holds the number of command-line arguments passed to a script or function.
key="$1"
case $key in # Match the value of the variable $key against different patterns or cases.
--datadir)
datadir="$2"
shift # Discard the current key and its associated value, allowing the loop to move to the next pair of arguments.
shift
;;
--vcfdir)
vcfdir="$2"
shift
shift
;;
--vcf2mafdir)
vcf2mafdir="$2"
shift
shift
;;
--ref_fasta)
ref_fasta="$2"
shift
shift
;;
--vep_path)
vep_path="$2"
shift
shift
;;
*)
usage
exit 1
;;
esac
done
# Check if the required arguments are provided by `-z` flag
if [[ -z $datadir ]] || [[ -z $vcfdir ]] || [[ -z $vcf2mafdir ]] || [[ -z $ref_fasta ]] || [[ -z $vep_path ]] || [[ -z $vep_data ]]; then
usage
exit 1
fi
echo ""
echo "Execute the bash file and run the vcf2maf.pl script for the conversion of a VCF file to a MAF file."
echo ""
# The `set -x` command is used to enable the shell's debugging mode.
# When this command is executed, the shell starts printing each command it executes along with their arguments and the results of variable substitutions.
set -x
# The VCF files are downloaded from the cluster and executed on the local machine using the code below.
# Four installed modules must be loaded if you want to run in a cluster.
module describe requirement_vcf2maf
module load SAMtools/1.15-foss-2020a
module load BCFtools/1.9-foss-2017a
module load HTSlib/1.15.1-GCC-9.3.0
module load Perl/5.28.0-GCCcore-7.3.0
module load Python/3.10.4-GCCcore-11.3.0
module load VEP/96.0-foss-2017a-Perl-5.24.2
# Download the VCF files from the cluster
# rsync -avz q874n@b06x-cnt3:/omics/groups/OE0290/internal/cbioportal_testing/cohort_analysis/vcf2maf/stdvcf $vcfdir
# Ensure the directories exist
mkdir -p $datadir/MAFfiles
mkdir -p $datadir/LSFscripts
mkdir -p $datadir/output_error
cd $vcfdir
find $vcfdir -name "*.stdzd.vcf" | while read -r file; do
if [ -f "$file" ]; then
dir=$(dirname "$file") # Print the directory of each file
PID=$(basename "$file" .stdzd.vcf) # Print the ID of each file
echo "Found STDZD VCF file: $dir/$PID.stdzd.vcf, ID: $PID"
STDVCFINFILE="${dir}/${PID}.stdzd.vcf"
BATCHINFILE="$datadir/LSFscripts/${PID}_batch.sh"
ERRORFILE="$datadir/output_error/${PID}_batch.err"
OUTFILE="$datadir/output_error/${PID}_batch.out"
sleep 10
# A batch file is a script or a text file that contains a sequence of commands or instructions to be executed by a computer's command-line interpreter or shell.
# It allows you to automate repetitive tasks or execute a series of commands in a specific order
# Create the batch file
cat <<EOT > "$BATCHINFILE"
#!/bin/bash
cd $vcf2mafdir
## execute program
perl vcf2maf.pl \
--input-vcf "$STDVCFINFILE" \
--output-maf "$datadir/MAFfiles/$PID.maf" \
--tumor-id "$PID" \
--normal-id "$PID" \
--ref-fasta "$ref_data" \
--vcf-tumor-id TUMOR \
--vcf-normal-id CONTROL \
--vep-path "$vep_path" \
--vep-data "$vep_data" \
--vep-overwrite \
--verbose \
1>"$OUTFILE" 2>"$ERRORFILE"
EOT
# Make the batch file executable
chmod +x "$BATCHINFILE"
# Execute the batch file using Bash
bash "$BATCHINFILE"
echo "Executed batch file for $PID"
fi
done
echo "Done."
sleep 10
echo ""
echo "Validate VCF input file to MAF output file and redirect the output to the file"
python $datadir/validate_vcf2maf_2023.py --datadir $datadir --vcfdir $vcfdir --mafdir $datadir/MAFfiles
# Upload the output result to a cluster.
# rsync -avz $datadir q874n@b06x-cnt3:/output
vcf2maf_cluster/raw_vcf/ 0000775 0001750 0001750 00000000000 14434145201 015774 5 ustar lucianhu lucianhu vcf2maf_cluster/raw_vcf/I002_002.stdzd.vcf 0000644 0001750 0001750 00000052156 14431663537 020643 0 ustar lucianhu lucianhu ##fileformat=VCFv4.1
##fileDate=20210510
##pancancerversion=1.0
##reference=<ID=hs37d5,Source=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz>;
##center="DKFZ"
##workflowName=DKFZ_SNV_workflow
##workflowVersion=1.0.0
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=GERMLINE,Number=0,Type=Flag,Description="Indicates if record is a germline mutation">
##INFO=<ID=UNCLEAR,Number=0,Type=Flag,Description="Indicates if the somatic status of a mutation is unclear">
##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, INS or DEL">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency in primary data, for each ALT allele, in the same order as listed">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="RMS Mapping Quality">
##INFO=<ID=1000G,Number=0,Type=Flag,Description="Indicates membership in 1000Genomes">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position in the sample">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases">
##FILTER=<ID=RE,Description="variant in UCSC_27Sept2013_RepeatMasker.bed.gz region and/or SimpleTandemRepeats_chr.bed.gz region, downloaded from UCSC genome browser and/or variant in segmental duplication region, annotated by annovar">
##FILTER=<ID=BL,Description="variant in DAC-Blacklist from ENCODE or in DUKE_EXCLUDED list, both downloaded from UCSC genome browser">
##FILTER=<ID=DP,Description="<= 5 reads total at position in tumor">
##FILTER=<ID=SB,Description="Strand bias of reads with mutant allele = zero reads on one strand">
##FILTER=<ID=TAC,Description="less than 6 reads in Tumor at position">
##FILTER=<ID=dbSNP,Description="variant in dbSNP135">
##FILTER=<ID=DB,Description="variant in 1000Genomes, ALL.wgs.phase1_integrated_calls.20101123.snps_chr.vcf.gz or dbSNP">
##FILTER=<ID=HSDEPTH,Description="variant in HiSeqDepthTop10Pct_chr.bed.gz region, downloaded from UCSC genome browser">
##FILTER=<ID=MAP,Description="variant overlaps a region from wgEncodeCrgMapabilityAlign100mer.bedGraph.gz:::--breakPointMode --aEndOffset=1 with a value below 0.5, punishment increases with a decreasing mapability">
##FILTER=<ID=SBAF,Description="Strand bias of reads with mutant allele = zero reads on one strand and variant allele frequency below 0.1">
##FILTER=<ID=FRQ,Description="variant allele frequency below 0.05">
##FILTER=<ID=TAR,Description="Only one alternative read in Tumor at position">
##FILTER=<ID=UNCLEAR,Description="Classification is unclear">
##FILTER=<ID=DPHIGH,Description="Too many reads mapped in control at this region">
##FILTER=<ID=DPLOWC,Description="Only 5 or less reads in control">
##FILTER=<ID=1PS,Description="Only two alternative reads, one on each strand">
##FILTER=<ID=ALTC,Description="Alternative reads in control">
##FILTER=<ID=ALTCFR,Description="Alternative reads in control and tumor allele frequency below 0.3">
##FILTER=<ID=FRC,Description="Variant allele frequency below 0.3 in germline call">
##FILTER=<ID=YALT,Description="Variant on Y chromosome with low allele frequency">
##FILTER=<ID=VAF,Description="Variant allele frequency in tumor < 5 times allele frequency in control">
##FILTER=<ID=BI,Description="Bias towards a PCR strand or sequencing strand">
##SAMPLE=<ID=CONTROL,SampleName=control_NA,Individual=NA,Description="Control">
##SAMPLE=<ID=TUMOR,SampleName=tumor_NA,Individual=NA,Description="Tumor">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CONTROL TUMOR
1 1254477 . G T . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60 GT:DP:DP4 0/0:130:48,82,0,0 0/1:102:27,36,18,21
1 34643608 . T C . DPHIGH SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:313:137,176,0,0 0/0:270:109,132,16,13
1 41236304 . A T . PASS SOMATIC;SNP;AF=0.00,0.36;MQ=60 GT:DP:DP4 0/0:253:173,79,0,0 0/1:190:92,29,52,17
1 109170721 . G T . PASS SOMATIC;SNP;AF=0.00,0.19;MQ=60 GT:DP:DP4 0/0:41:41,0,0,0 0/1:37:30,0,7,0
1 120471778 . C T . PASS SOMATIC;SNP;AF=0.00,0.72;MQ=60 GT:DP:DP4 0/0:207:120,87,0,0 0/1:115:29,3,65,18
1 152059804 . A G . PASS SOMATIC;SNP;AF=0.01,0.15;MQ=60 GT:DP:DP4 0/0:182:91,90,0,1 0/0:236:105,95,18,18
1 183209509 . G A . PASS SOMATIC;SNP;AF=0.00,0.14;MQ=60 GT:DP:DP4 0/0:134:26,108,0,0 0/0:245:45,165,8,27
1 186320375 . T C . PASS SOMATIC;SNP;AF=0.00,0.30;MQ=60 GT:DP:DP4 0/0:105:86,19,0,0 0/1:209:133,13,57,6
1 201166270 . C T . PASS SOMATIC;SNP;AF=0.00,0.07;MQ=60 GT:DP:DP4 0/0:97:64,33,0,0 0/0:174:114,48,9,3
1 201435057 . C T . PASS SOMATIC;SNP;AF=0.00,0.07;MQ=60 GT:DP:DP4 0/0:89:51,38,0,0 0/0:161:87,63,5,6
1 203053732 . A G . PASS SOMATIC;SNP;AF=0.00,0.14;MQ=60 GT:DP:DP4 0/0:51:28,23,0,0 0/1:72:45,17,6,4
1 205027917 . C A . PASS SOMATIC;SNP;AF=0.00,0.17;MQ=60 GT:DP:DP4 0/0:29:4,25,0,0 0/1:36:2,28,1,5
1 214575108 . G T . PASS SOMATIC;SNP;AF=0.00,0.14;MQ=60 GT:DP:DP4 0/0:146:58,88,0,0 0/0:239:102,103,16,18
1 225562487 . G A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:173:83,90,0,0 0/1:258:102,101,25,30
1 247062663 . A C . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:72:51,21,0,0 0/1:86:54,22,7,3
1 249150578 . C G . PASS SOMATIC;SNP;AF=0.00,0.19;MQ=60 GT:DP:DP4 0/0:86:71,15,0,0 0/1:128:90,14,22,2
2 26696156 . G A . PASS SOMATIC;SNP;AF=0.00,0.41;MQ=60 GT:DP:DP4 0/0:115:56,59,0,0 0/1:109:33,31,28,17
2 30791183 . G A . PASS SOMATIC;SNP;AF=0.00,0.16;MQ=60 GT:DP:DP4 0/0:17:0,17,0,0 0/1:38:0,32,0,6
2 55615954 . T A . PASS SOMATIC;SNP;AF=0.00,0.07;MQ=60 GT:DP:DP4 0/0:85:37,48,0,0 0/0:90:41,43,2,4
2 91777710 rs7596249_91777710 C T . PASS SOMATIC;SNP;AF=0.00,0.16;MQ=55;DB GT:DP:DP4 0/0:24:11,13,0,0 0/1:43:23,13,4,3
2 118578807 . A T . PASS SOMATIC;SNP;AF=0.00,0.25;MQ=59 GT:DP:DP4 0/0:74:67,7,0,0 0/1:81:57,4,20,0
2 201243028 . C T . PASS SOMATIC;SNP;AF=0.00,0.30;MQ=60 GT:DP:DP4 0/0:53:32,21,0,0 0/1:70:30,19,14,7
3 9984502 . G C . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=60 GT:DP:DP4 0/0:105:37,68,0,0 0/1:115:29,55,15,16
3 41266113 rs121913403_41266113 C T . PASS SOMATIC;SNP;AF=0.00,0.31;MQ=60;DB GT:DP:DP4 0/0:71:32,39,0,0 0/1:84:34,24,13,13
3 44763977 . C T . PASS SOMATIC;SNP;AF=0.00,0.48;MQ=60 GT:DP:DP4 0/0:22:1,21,0,0 0/1:23:0,12,0,11
3 50326005 . T C . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:237:125,112,0,0 0/0:300:157,113,24,6
3 51430086 . G T . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:200:101,99,0,0 0/0:296:148,134,6,8
3 52399146 . C T . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=60 GT:DP:DP4 0/0:12:1,11,0,0 0/1:22:1,15,0,6
3 57140039 . G A . PASS SOMATIC;SNP;AF=0.00,0.22;MQ=60 GT:DP:DP4 0/0:210:145,65,0,0 0/1:215:135,33,28,19
3 58318708 . G A . PASS SOMATIC;SNP;AF=0.00,0.51;MQ=60 GT:DP:DP4 0/0:26:12,14,0,0 0/1:45:15,7,15,8
3 67991756 rs62247216_67991756 T C . PASS SOMATIC;SNP;AF=0.00,0.67;MQ=60;DB;1000G GT:DP:DP4 0/0:11:5,6,0,0 0/1:9:2,1,1,5
3 124748359 . G A . PASS SOMATIC;SNP;AF=0.00,0.35;MQ=60 GT:DP:DP4 0/0:49:12,37,0,0 0/1:65:9,33,4,19
3 169650997 . G A . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60 GT:DP:DP4 0/0:37:11,26,0,0 0/1:41:19,16,3,3
3 183777753 . A T . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=57 GT:DP:DP4 0/0:26:9,17,0,0 0/1:30:14,8,3,5
3 186618158 . T A . PASS SOMATIC;SNP;AF=0.00,0.23;MQ=57 GT:DP:DP4 0/0:19:14,5,0,0 0/1:26:12,8,3,3
3 186618181 rs397839855_186618181 A G . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=56;DB GT:DP:DP4 0/0:23:14,9,0,0 0/1:28:8,15,2,3
4 146572340 . T C . PASS SOMATIC;SNP;AF=0.00,0.35;MQ=60 GT:DP:DP4 0/0:90:2,88,0,0 0/1:82:9,44,4,25
4 147177983 . G A . PASS SOMATIC;SNP;AF=0.00,0.67;MQ=60 GT:DP:DP4 0/0:79:65,14,0,0 0/1:46:14,1,27,4
4 160272153 . G T . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:90:56,34,0,0 0/1:58:37,14,6,1
5 916975 rs72703199_916975 G A . PASS SOMATIC;SNP;AF=0.00,0.57;MQ=60;DB;1000G GT:DP:DP4 0/0:12:11,1,0,0 0/1:14:6,0,8,0
5 54410184 rs145015277_54410184 G A . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60;DB;1000G GT:DP:DP4 0/0:28:1,27,0,0 0/1:36:2,16,0,18
5 127873189 . C T . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=60 GT:DP:DP4 0/0:103:56,47,0,0 0/1:126:56,45,12,13
5 137713463 . A C . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:218:134,84,0,0 0/0:254:151,78,20,5
5 149578825 . A G . PASS SOMATIC;SNP;AF=0.00,0.26;MQ=60 GT:DP:DP4 0/0:73:50,23,0,0 0/1:77:30,27,14,6
5 176024321 . C T . PASS SOMATIC;SNP;AF=0.00,0.33;MQ=60 GT:DP:DP4 0/0:16:6,10,0,0 0/1:18:6,6,4,2
5 180219704 . C A . PASS SOMATIC;SNP;AF=0.00,0.08;MQ=60 GT:DP:DP4 0/0:50:10,40,0,0 0/0:90:15,68,2,5
6 13470814 . T C . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=60 GT:DP:DP4 0/0:149:75,74,0,0 0/0:177:88,73,15,1
6 31603295 . G A . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:147:89,57,0,0 0/0:193:104,78,5,6
6 32489734 rs115563246_32489734 G A . PASS SOMATIC;SNP;AF=0.01,0.05;MQ=57;DB;1000G GT:DP:DP4 0/0:101:72,28,1,0 0/0:111:84,21,3,3
6 32489735 rs115817940_32489735 G T . PASS SOMATIC;SNP;AF=0.01,0.05;MQ=57;DB;1000G GT:DP:DP4 0/0:100:72,27,1,0 0/0:111:81,24,3,3
6 33541717 . C T . RE;DPHIGH SOMATIC;SNP;AF=0.00,0.44;MQ=60 GT:DP:DP4 0/0:274:131,143,0,0 0/1:256:69,75,46,66
6 40357778 . G C . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:6:2,4,0,0 0/1:6:1,2,1,2
6 42571276 . A G . PASS SOMATIC;SNP;AF=0.00,0.48;MQ=60 GT:DP:DP4 0/0:25:23,2,0,0 0/1:31:14,2,15,0
6 90504442 . T C . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:54:33,21,0,0 0/1:56:39,10,6,1
6 166578193 . A T . PASS SOMATIC;SNP;AF=0.00,0.19;MQ=60 GT:DP:DP4 0/0:78:32,46,0,0 0/1:84:27,41,6,10
7 43917995 . G C . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:187:116,71,0,0 0/0:245:165,55,16,9
7 44733393 . G T . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=60 GT:DP:DP4 0/0:106:89,17,0,0 0/0:171:146,10,14,1
7 48411984 rs200787053_48411984 G A . PASS SOMATIC;SNP;AF=0.00,0.39;MQ=60;DB;1000G GT:DP:DP4 0/0:230:101,129,0,0 0/1:267:95,67,61,44
7 99621666 . A G . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=60 GT:DP:DP4 0/0:116:75,41,0,0 0/0:156:97,45,9,5
7 99951290 . G A . PASS SOMATIC;SNP;AF=0.00,0.22;MQ=60 GT:DP:DP4 0/0:90:46,44,0,0 0/1:86:43,24,11,8
7 102993288 . G T . PASS SOMATIC;SNP;AF=0.00,0.08;MQ=60 GT:DP:DP4 0/0:83:67,16,0,0 0/0:98:79,11,7,1
7 104751135 . G T . PASS SOMATIC;SNP;AF=0.00,0.23;MQ=60 GT:DP:DP4 0/0:165:109,56,0,0 0/1:207:101,58,30,18
7 105250889 . T C . PASS SOMATIC;SNP;AF=0.00,0.24;MQ=60 GT:DP:DP4 0/0:77:42,35,0,0 0/1:100:48,28,19,5
7 139813109 . T C . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60 GT:DP:DP4 0/0:35:35,0,0,0 0/1:42:26,0,16,0
7 149477511 . T C . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=60 GT:DP:DP4 0/0:77:24,53,0,0 0/1:85:14,54,7,10
8 11891331 . C T . PASS SOMATIC;SNP;AF=0.00,0.32;MQ=60 GT:DP:DP4 0/0:16:14,2,0,0 0/1:25:14,3,5,3
8 27320606 . C G . PASS SOMATIC;SNP;AF=0.00,0.19;MQ=60 GT:DP:DP4 0/0:76:47,29,0,0 0/1:118:55,41,13,9
8 39525590 . C A . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=60 GT:DP:DP4 0/0:179:109,70,0,0 0/0:177:123,38,13,3
8 48883203 rs144129405_48883203 G C . PASS SOMATIC;SNP;AF=0.00,0.08;MQ=60;DB GT:DP:DP4 0/0:78:29,49,0,0 0/0:86:35,44,3,4
8 62627004 rs3750279_62627004 A G . PASS SOMATIC;SNP;AF=0.00,0.58;MQ=60;DB;1000G GT:DP:DP4 0/0:12:3,9,0,0 0/1:12:1,4,0,7
8 100287403 . G A . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:91:49,42,0,0 0/0:130:81,33,8,8
8 144650901 . G A . PASS SOMATIC;SNP;AF=0.00,0.34;MQ=60 GT:DP:DP4 0/0:9:2,7,0,0 0/1:41:4,23,1,13
8 145999392 . C A . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:83:43,40,0,0 0/0:109:50,54,3,2
9 73151313 . T G . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:96:34,62,0,0 0/0:101:35,60,1,5
9 76090222 . G A . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=60 GT:DP:DP4 0/0:55:35,20,0,0 0/0:64:53,5,4,2
9 84235856 . A G . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:106:33,73,0,0 0/1:126:35,68,12,11
9 88514525 . C T . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=60 GT:DP:DP4 0/0:36:10,26,0,0 0/1:41:9,21,2,9
9 88886935 . T A . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=56 GT:DP:DP4 0/0:30:29,1,0,0 0/1:39:32,1,6,0
9 135275299 . G C . PASS SOMATIC;SNP;AF=0.00,0.47;MQ=60 GT:DP:DP4 0/0:9:9,0,0,0 0/1:15:8,0,7,0
9 140682296 . C T . PASS SOMATIC;SNP;AF=0.00,0.36;MQ=60 GT:DP:DP4 0/0:19:4,15,0,0 0/1:22:3,11,1,7
10 13167946 . G T . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:110:68,42,0,0 0/1:68:34,26,3,5
10 22055113 . A G . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:65:62,3,0,0 0/0:89:77,0,12,0
10 25888046 . C A . PASS SOMATIC;SNP;AF=0.00,0.36;MQ=60 GT:DP:DP4 0/0:119:55,64,0,0 0/1:160:59,44,33,24
10 29751496 rs113437893_29751496 T A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=56;DB GT:DP:DP4 0/0:26:0,26,0,0 0/0:29:0,23,0,6
10 33502173 . G A . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:152:83,68,0,0 0/0:197:121,66,8,2
10 45733782 . C G . PASS SOMATIC;SNP;AF=0.00,0.41;MQ=60 GT:DP:DP4 0/0:91:25,66,0,0 0/1:134:18,61,16,39
10 79743635 . C A . PASS SOMATIC;SNP;AF=0.00,0.22;MQ=60 GT:DP:DP4 0/0:73:67,6,0,0 0/1:108:79,5,21,3
10 99349881 . A T . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:204:101,103,0,0 0/0:232:113,104,10,5
10 115917333 . G A . PASS SOMATIC;SNP;AF=0.00,0.39;MQ=60 GT:DP:DP4 0/0:45:30,15,0,0 0/1:36:18,4,10,4
10 116038622 rs374045265_116038622 C T . PASS SOMATIC;SNP;AF=0.00,0.40;MQ=60;DB GT:DP:DP4 0/0:20:5,15,0,0 0/1:15:3,6,1,5
10 123274873 . C T . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:31:2,29,0,0 0/1:55:0,45,1,9
11 3113658 . T A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:45:38,7,0,0 0/1:48:34,4,10,0
11 22362991 . C T . PASS SOMATIC;SNP;AF=0.00,0.73;MQ=60 GT:DP:DP4 0/0:22:22,0,0,0 0/1:15:4,0,11,0
11 66512563 . C A . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:10:0,10,0,0 0/1:12:0,6,1,5
11 74457097 . C A . PASS SOMATIC;SNP;AF=0.03,0.19;MQ=56 GT:DP:DP4 0/0:32:27,4,0,1 0/1:31:23,2,3,3
11 75150945 . A T . PASS SOMATIC;SNP;AF=0.00,0.70;MQ=60 GT:DP:DP4 0/0:116:78,38,0,0 0/1:66:14,6,31,15
11 98436700 . T C . PASS SOMATIC;SNP;AF=0.00,0.39;MQ=60 GT:DP:DP4 0/0:64:36,28,0,0 0/1:31:13,6,8,4
11 99827574 . C T . PASS SOMATIC;SNP;AF=0.00,0.08;MQ=60 GT:DP:DP4 0/0:229:157,72,0,0 0/0:135:92,32,9,2
11 114442121 . T C . PASS SOMATIC;SNP;AF=0.00,0.63;MQ=60 GT:DP:DP4 0/0:143:80,63,0,0 0/1:108:17,23,36,32
11 119340642 . G A . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:100:34,66,0,0 0/1:137:17,69,13,38
11 123624292 . T A . PASS SOMATIC;SNP;AF=0.00,0.33;MQ=60 GT:DP:DP4 0/0:63:51,12,0,0 0/1:61:29,12,17,3
11 123624925 . A G . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60 GT:DP:DP4 0/0:114:83,31,0,0 0/1:137:73,12,40,12
11 129753990 . T C . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:214:129,85,0,0 0/0:269:129,92,32,16
12 7288517 . A G . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:34:5,29,0,0 0/1:34:3,27,1,3
12 13717053 . C T . PASS SOMATIC;SNP;AF=0.00,0.34;MQ=60 GT:DP:DP4 0/0:236:88,147,0,1 0/1:290:79,112,46,53
12 49717889 . G T . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:121:48,73,0,0 0/0:171:82,72,2,15
12 52106249 . G C . PASS SOMATIC;SNP;AF=0.00,0.26;MQ=60 GT:DP:DP4 0/0:107:68,39,0,0 0/1:141:80,25,24,12
12 58016868 rs138048824_58016868 C T . PASS SOMATIC;SNP;AF=0.00,0.36;MQ=60;DB GT:DP:DP4 0/0:103:25,78,0,0 0/1:118:14,62,9,33
13 20608352 rs61952376_20608352 C G . PASS SOMATIC;SNP;AF=0.02,0.10;MQ=60;DB GT:DP:DP4 0/0:57:41,15,1,0 0/0:73:55,11,5,2
13 24468568 . A C . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=46 GT:DP:DP4 0/0:62:48,14,0,0 0/0:102:83,13,5,1
13 36413100 . C T . PASS SOMATIC;SNP;AF=0.00,0.41;MQ=60 GT:DP:DP4 0/0:39:31,8,0,0 0/1:51:27,3,20,1
13 52693546 . G A . PASS SOMATIC;SNP;AF=0.00,0.14;MQ=60 GT:DP:DP4 0/0:79:28,51,0,0 0/1:96:35,48,10,3
13 102025394 . G A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:55:47,8,0,0 0/1:63:42,8,11,2
13 110434478 . C A . PASS SOMATIC;SNP;AF=0.00,0.24;MQ=60 GT:DP:DP4 0/0:119:52,67,0,0 0/1:148:67,45,23,13
14 20470866 . G A . PASS SOMATIC;SNP;AF=0.00,0.23;MQ=60 GT:DP:DP4 0/0:281:131,150,0,0 0/1:362:130,147,47,38
14 45653080 . T C . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:161:46,115,0,0 0/0:151:46,89,3,13
14 54907976 . C T . PASS SOMATIC;SNP;AF=0.00,0.30;MQ=60 GT:DP:DP4 0/0:65:35,30,0,0 0/1:67:28,19,14,6
14 77492787 . C T . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:219:150,69,0,0 0/0:273:170,76,17,10
15 42703963 . T C . PASS SOMATIC;SNP;AF=0.00,0.28;MQ=60 GT:DP:DP4 0/0:99:75,24,0,0 0/1:97:55,15,25,2
15 58834964 . T C . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:51:7,44,0,0 0/1:75:7,58,0,10
15 63349326 . G A . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=60 GT:DP:DP4 0/0:25:2,23,0,0 0/1:55:6,38,3,8
15 89736408 . C G . PASS SOMATIC;SNP;AF=0.00,0.40;MQ=60 GT:DP:DP4 0/0:219:118,101,0,0 0/1:269:97,65,70,37
16 721267 . T C . RE;DPHIGH SOMATIC;SNP;AF=0.00,0.09;MQ=60 GT:DP:DP4 0/0:221:74,147,0,0 0/0:276:92,158,13,13
16 30780463 . G T . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:136:98,38,0,0 0/0:194:153,32,7,2
16 50261803 . C G . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:216:82,134,0,0 0/1:256:97,112,27,20
17 7324245 . A G . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:287:142,145,0,0 0/0:388:219,127,19,23
17 7690186 . G A . PASS SOMATIC;SNP;AF=0.00,0.45;MQ=60 GT:DP:DP4 0/0:139:83,56,0,0 0/1:190:88,16,67,19
17 9448391 . T G . PASS SOMATIC;SNP;AF=0.00,0.23;MQ=60 GT:DP:DP4 0/0:146:132,14,0,0 0/1:186:138,6,41,1
17 17286993 rs13003_17286993 C T . PASS SOMATIC;SNP;AF=0.00,0.24;MQ=49;DB GT:DP:DP4 0/0:17:8,9,0,0 0/1:42:12,20,0,10
17 26209967 . C T . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:67:39,28,0,0 0/1:78:40,22,13,3
17 27901684 . G T . PASS SOMATIC;SNP;AF=0.00,0.16;MQ=60 GT:DP:DP4 0/0:74:37,37,0,0 0/1:102:49,37,10,6
17 34091364 . C T . PASS SOMATIC;SNP;AF=0.00,0.31;MQ=60 GT:DP:DP4 0/0:23:13,10,0,0 0/1:32:19,3,6,4
17 37619317 . G T . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:197:90,107,0,0 0/0:254:128,93,21,12
17 57076677 . A G . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=60 GT:DP:DP4 0/0:119:86,33,0,0 0/1:145:101,15,26,3
17 79967315 . G A . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=60 GT:DP:DP4 0/0:45:30,15,0,0 0/0:66:50,10,2,4
18 34904319 rs622476_34904319 A G . PASS SOMATIC;SNP;AF=0.00,0.78;MQ=60;DB;1000G GT:DP:DP4 0/0:13:4,9,0,0 0/1:9:1,1,4,3
18 34904370 rs622090_34904370 A G . PASS SOMATIC;SNP;AF=0.00,0.67;MQ=60;DB;1000G GT:DP:DP4 0/0:10:1,9,0,0 0/1:9:1,2,3,3
18 44139159 . C T . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60 GT:DP:DP4 0/0:300:125,175,0,0 0/1:321:112,88,56,65
18 47463635 . T G . PASS SOMATIC;SNP;AF=0.00,0.19;MQ=60 GT:DP:DP4 0/0:97:79,18,0,0 0/1:126:90,12,21,3
18 67817960 . C G . PASS SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:48:8,40,0,0 0/1:52:3,27,6,16
19 1051953 . T C . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:19:12,7,0,0 0/1:38:13,11,10,4
19 9629611 . C A . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:13:9,4,0,0 0/1:16:2,6,3,5
19 38653055 . G A . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:25:0,25,0,0 0/1:34:2,26,2,4
19 55350831 . G A . PASS SOMATIC;SNP;AF=0.00,0.65;MQ=60 GT:DP:DP4 0/0:46:41,5,0,0 0/1:43:15,0,26,2
20 17594879 . C T . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:72:40,32,0,0 0/0:109:56,48,2,3
20 32663637 . G A . PASS SOMATIC;SNP;AF=0.00,0.30;MQ=60 GT:DP:DP4 0/0:25:25,0,0,0 0/1:30:20,1,8,1
20 35282083 . C T . PASS SOMATIC;SNP;AF=0.00,0.25;MQ=60 GT:DP:DP4 0/0:38:6,32,0,0 0/1:55:9,32,1,13
20 35860582 . G A . PASS SOMATIC;SNP;AF=0.00,0.28;MQ=60 GT:DP:DP4 0/0:77:70,7,0,0 0/1:128:89,3,35,1
20 36024711 . T C . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60 GT:DP:DP4 0/0:54:17,37,0,0 0/1:74:28,35,6,5
20 36854161 . T A . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:28:6,22,0,0 0/1:38:4,29,2,3
20 48346218 . T A . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:21:12,9,0,0 0/1:23:13,7,2,1
20 54579109 . C A . PASS SOMATIC;SNP;AF=0.00,0.31;MQ=60 GT:DP:DP4 0/0:83:31,52,0,0 0/1:105:29,43,17,16
21 19713842 . G T . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:121:24,97,0,0 0/0:151:27,108,1,15
21 19713848 . A G . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:116:23,93,0,0 0/0:142:22,104,1,15
21 28296901 . G T . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:268:110,158,0,0 0/0:295:129,151,9,6
21 40768954 . A G . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:69:5,64,0,0 0/1:79:6,44,2,27
22 18020393 . G A . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:90:45,45,0,0 0/0:121:70,37,9,5
22 24717334 rs199596465_24717334 G A . PASS SOMATIC;SNP;AF=0.00,0.39;MQ=60;DB GT:DP:DP4 0/0:228:93,135,0,0 0/1:243:81,67,50,45
22 30865337 rs9620997_30865337 G A . PASS SOMATIC;SNP;AF=0.00,0.67;MQ=60;DB;1000G GT:DP:DP4 0/0:10:8,2,0,0 0/1:9:1,2,5,1
22 30866380 rs2269964_30866380 T C . PASS SOMATIC;SNP;AF=0.00,0.36;MQ=60;DB;1000G GT:DP:DP4 0/0:12:4,8,0,0 0/1:11:3,4,1,3
22 37407142 . C T . PASS SOMATIC;SNP;AF=0.00,0.26;MQ=60 GT:DP:DP4 0/0:41:34,7,0,0 0/1:43:31,1,8,3
22 42139012 . C T . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60 GT:DP:DP4 0/0:10:10,0,0,0 0/1:21:12,0,8,1
X 37961758 . A T . PASS SOMATIC;SNP;AF=0.00,0.35;MQ=60 GT:DP:DP4 0/0:103:15,88,0,0 0/1:158:8,94,9,47
X 48834736 . C T . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60 GT:DP:DP4 0/0:117:56,61,0,0 0/1:130:44,30,28,28
X 53173077 . C T . PASS SOMATIC;SNP;AF=0.00,0.40;MQ=60 GT:DP:DP4 0/0:23:9,14,0,0 0/1:20:4,8,1,7
X 55479467 . A C . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:92:14,78,0,0 0/0:148:33,98,4,13
X 63551413 . T C . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60 GT:DP:DP4 0/0:71:66,5,0,0 0/1:85:71,1,11,2
X 70613023 . T C . PASS SOMATIC;SNP;AF=0.00,0.39;MQ=60 GT:DP:DP4 0/0:67:11,56,0,0 0/1:89:13,41,7,28
X 105193567 . C T . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:177:133,44,0,0 0/0:216:174,20,20,2
X 112048228 . G A . PASS SOMATIC;SNP;AF=0.00,0.34;MQ=60 GT:DP:DP4 0/0:68:48,20,0,0 0/1:89:44,15,24,6
X 113625152 . C T . PASS SOMATIC;SNP;AF=0.00,0.51;MQ=60 GT:DP:DP4 0/0:22:11,11,0,0 0/1:35:10,7,18,0
X 149638222 . G A . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:90:48,42,0,0 0/0:116:73,37,4,2
vcf2maf_cluster/raw_vcf/I002_003.stdzd.vcf 0000644 0001750 0001750 00000035763 14431663537 020651 0 ustar lucianhu lucianhu ##fileformat=VCFv4.1
##fileDate=20210510
##pancancerversion=1.0
##reference=<ID=hs37d5,Source=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz>;
##center="DKFZ"
##workflowName=DKFZ_SNV_workflow
##workflowVersion=1.0.0
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=GERMLINE,Number=0,Type=Flag,Description="Indicates if record is a germline mutation">
##INFO=<ID=UNCLEAR,Number=0,Type=Flag,Description="Indicates if the somatic status of a mutation is unclear">
##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, INS or DEL">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency in primary data, for each ALT allele, in the same order as listed">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="RMS Mapping Quality">
##INFO=<ID=1000G,Number=0,Type=Flag,Description="Indicates membership in 1000Genomes">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position in the sample">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases">
##FILTER=<ID=RE,Description="variant in UCSC_27Sept2013_RepeatMasker.bed.gz region and/or SimpleTandemRepeats_chr.bed.gz region, downloaded from UCSC genome browser and/or variant in segmental duplication region, annotated by annovar">
##FILTER=<ID=BL,Description="variant in DAC-Blacklist from ENCODE or in DUKE_EXCLUDED list, both downloaded from UCSC genome browser">
##FILTER=<ID=DP,Description="<= 5 reads total at position in tumor">
##FILTER=<ID=SB,Description="Strand bias of reads with mutant allele = zero reads on one strand">
##FILTER=<ID=TAC,Description="less than 6 reads in Tumor at position">
##FILTER=<ID=dbSNP,Description="variant in dbSNP135">
##FILTER=<ID=DB,Description="variant in 1000Genomes, ALL.wgs.phase1_integrated_calls.20101123.snps_chr.vcf.gz or dbSNP">
##FILTER=<ID=HSDEPTH,Description="variant in HiSeqDepthTop10Pct_chr.bed.gz region, downloaded from UCSC genome browser">
##FILTER=<ID=MAP,Description="variant overlaps a region from wgEncodeCrgMapabilityAlign100mer.bedGraph.gz:::--breakPointMode --aEndOffset=1 with a value below 0.5, punishment increases with a decreasing mapability">
##FILTER=<ID=SBAF,Description="Strand bias of reads with mutant allele = zero reads on one strand and variant allele frequency below 0.1">
##FILTER=<ID=FRQ,Description="variant allele frequency below 0.05">
##FILTER=<ID=TAR,Description="Only one alternative read in Tumor at position">
##FILTER=<ID=UNCLEAR,Description="Classification is unclear">
##FILTER=<ID=DPHIGH,Description="Too many reads mapped in control at this region">
##FILTER=<ID=DPLOWC,Description="Only 5 or less reads in control">
##FILTER=<ID=1PS,Description="Only two alternative reads, one on each strand">
##FILTER=<ID=ALTC,Description="Alternative reads in control">
##FILTER=<ID=ALTCFR,Description="Alternative reads in control and tumor allele frequency below 0.3">
##FILTER=<ID=FRC,Description="Variant allele frequency below 0.3 in germline call">
##FILTER=<ID=YALT,Description="Variant on Y chromosome with low allele frequency">
##FILTER=<ID=VAF,Description="Variant allele frequency in tumor < 5 times allele frequency in control">
##FILTER=<ID=BI,Description="Bias towards a PCR strand or sequencing strand">
##SAMPLE=<ID=CONTROL,SampleName=control_NA,Individual=NA,Description="Control">
##SAMPLE=<ID=TUMOR,SampleName=tumor_NA,Individual=NA,Description="Tumor">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CONTROL TUMOR
1 53238161 . C G . PASS SOMATIC;SNP;AF=0.00,0.22;MQ=59 GT:DP:DP4 0/0:9:7,2,0,0 0/1:18:11,3,3,1
1 120491740 . C A . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60 GT:DP:DP4 0/0:182:61,121,0,0 0/0:213:57,125,8,23
1 157678883 . G A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:37:35,2,0,0 0/1:38:29,1,7,1
1 158450075 . T C . DPHIGH SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:378:179,199,0,0 0/0:404:158,197,29,20
1 174978835 . T A . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:23:23,0,0,0 0/0:64:57,0,7,0
1 205555254 . G C . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=60 GT:DP:DP4 0/0:48:31,17,0,0 0/1:26:14,5,5,2
1 226026241 rs4149223_226026241 C G . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60;DB;1000G GT:DP:DP4 0/0:11:9,2,0,0 0/1:16:10,0,6,0
1 228491150 . T G . PASS SOMATIC;SNP;AF=0.00,0.14;MQ=60 GT:DP:DP4 0/0:35:19,16,0,0 0/1:56:36,12,7,1
2 8918890 . A G . PASS SOMATIC;SNP;AF=0.00,0.24;MQ=60 GT:DP:DP4 0/0:188:50,138,0,0 0/1:164:29,96,10,29
2 9599764 . A T . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=59 GT:DP:DP4 0/0:41:2,39,0,0 0/0:62:0,54,0,8
2 131904373 . C T . PASS SOMATIC;SNP;AF=0.00,0.16;MQ=60 GT:DP:DP4 0/0:81:15,66,0,0 0/1:100:13,71,2,14
2 135958040 . C T . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:212:66,146,0,0 0/0:215:62,140,7,6
2 198540308 . T A . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:16:0,16,0,0 0/0:34:1,27,0,6
2 211476731 . A T . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60 GT:DP:DP4 0/0:30:29,0,0,0 0/0:41:34,1,6,0
2 211476744 . A T . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:39:39,0,0,0 0/0:54:48,0,6,0
2 213872832 . G A . PASS SOMATIC;SNP;AF=0.02,0.10;MQ=60 GT:DP:DP4 0/0:42:7,34,0,1 0/0:58:17,35,0,6
3 33059855 . G A . PASS SOMATIC;SNP;AF=0.02,0.15;MQ=60 GT:DP:DP4 0/0:43:39,3,1,0 0/0:39:33,0,6,0
3 52443857 . C T . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:52:19,33,0,0 0/1:43:12,22,2,7
3 127106542 . G C . PASS SOMATIC;SNP;AF=0.01,0.07;MQ=60 GT:DP:DP4 0/0:83:61,21,1,0 0/0:106:82,17,6,1
3 127106591 . T C . PASS SOMATIC;SNP;AF=0.01,0.06;MQ=60 GT:DP:DP4 0/0:138:85,52,1,0 0/0:155:113,33,7,2
3 139301854 . G A . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=52 GT:DP:DP4 0/0:34:18,16,0,0 0/1:50:25,15,8,2
4 1389247 . T C . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=58 GT:DP:DP4 0/0:104:58,46,0,0 0/0:124:71,47,2,4
4 15504352 . T C . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:79:65,14,0,0 0/0:86:72,4,9,1
4 178274911 . G A . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:42:3,39,0,0 0/0:51:1,44,0,6
5 137089785 . G A . PASS SOMATIC;SNP;AF=0.00,0.25;MQ=60 GT:DP:DP4 0/0:152:73,79,0,0 0/1:151:61,53,14,23
5 140175958 . C T . PASS SOMATIC;SNP;AF=0.00,0.16;MQ=60 GT:DP:DP4 0/0:110:38,72,0,0 0/1:114:37,59,8,10
5 173416528 . T C . PASS SOMATIC;SNP;AF=0.00,0.17;MQ=60 GT:DP:DP4 0/0:117:58,59,0,0 0/1:88:47,26,8,7
6 29770073 . G A . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=56 GT:DP:DP4 0/0:12:8,4,0,0 0/1:11:6,2,1,2
6 29770078 . G C . PASS SOMATIC;SNP;AF=0.00,0.23;MQ=55 GT:DP:DP4 0/0:12:8,4,0,0 0/1:13:6,4,1,2
6 29770080 . C A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=55 GT:DP:DP4 0/0:13:9,4,0,0 0/1:14:7,4,1,2
6 29770087 . A C . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=55 GT:DP:DP4 0/0:15:11,4,0,0 0/1:15:8,4,1,2
6 29864627 . G C . PASS SOMATIC;SNP;AF=0.03,0.22;MQ=57 GT:DP:DP4 0/0:31:23,7,0,1 0/1:32:16,9,5,2
6 29864632 . C A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=57 GT:DP:DP4 0/0:32:25,7,0,0 0/1:34:18,9,5,2
6 29864634 . A G . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=57 GT:DP:DP4 0/0:32:25,7,0,0 0/1:34:18,9,5,2
6 29864635 . G T . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=57 GT:DP:DP4 0/0:32:25,7,0,0 0/1:35:19,9,5,2
6 29864637 . G A . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=57 GT:DP:DP4 0/0:32:25,7,0,0 0/1:35:20,8,5,2
6 29864639 . C G . PASS SOMATIC;SNP;AF=0.03,0.20;MQ=57 GT:DP:DP4 0/0:33:25,7,1,0 0/1:35:20,8,5,2
6 29865591 rs73725500_29865591 G A . PASS SOMATIC;SNP;AF=0.00,0.22;MQ=57;DB GT:DP:DP4 0/0:11:2,9,0,0 0/1:18:3,11,1,3
6 64431072 . G A . PASS SOMATIC;SNP;AF=0.00,0.08;MQ=60 GT:DP:DP4 0/0:239:158,81,0,0 0/0:253:170,63,12,8
6 76589671 . T G . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60 GT:DP:DP4 0/0:137:59,78,0,0 0/1:130:43,68,8,11
7 40234737 . G T . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:39:0,38,0,0 0/0:81:0,72,0,9
7 73117374 . A G . PASS SOMATIC;SNP;AF=0.00,0.14;MQ=60 GT:DP:DP4 0/0:47:3,44,0,0 0/0:83:5,66,0,12
7 100656361 . G C . PASS SOMATIC;SNP;AF=0.00,0.23;MQ=60 GT:DP:DP4 0/0:132:33,99,0,0 0/1:144:36,75,8,25
7 107688584 . T A . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=59 GT:DP:DP4 0/0:37:0,37,0,0 0/0:59:0,50,0,9
7 148702265 . G C . PASS SOMATIC;SNP;AF=0.00,0.19;MQ=60 GT:DP:DP4 0/0:64:49,15,0,0 0/1:99:62,18,14,5
7 157261156 . G A . PASS SOMATIC;SNP;AF=0.00,0.28;MQ=60 GT:DP:DP4 0/0:7:5,2,0,0 0/1:32:22,1,9,0
8 2857753 rs183144808_2857753 C T . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60;DB;1000G GT:DP:DP4 0/0:19:0,19,0,0 0/1:39:0,31,0,8
8 87680282 rs16916632_87680282 C T . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=60;DB;1000G GT:DP:DP4 0/0:280:153,127,0,0 0/0:348:164,151,20,13
9 116759865 rs12238713_116759865 C A . PASS SOMATIC;SNP;AF=0.03,0.27;MQ=60;DB;1000G GT:DP:DP4 0/0:37:20,16,1,0 0/1:33:16,8,7,2
9 137314411 . T C . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:93:27,66,0,0 0/0:132:47,79,1,5
10 45938676 . C T . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:153:44,108,0,0 0/0:187:75,101,2,9
10 73044497 . C T . PASS SOMATIC;SNP;AF=0.02,0.11;MQ=60 GT:DP:DP4 0/0:45:35,9,1,0 0/0:54:39,9,6,0
10 73044503 . G T . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:49:38,11,0,0 0/0:55:40,9,6,0
10 73571651 . A C . PASS SOMATIC;SNP;AF=0.03,0.17;MQ=60 GT:DP:DP4 0/0:37:31,5,1,0 0/0:65:50,4,11,0
11 710246 . G A . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60 GT:DP:DP4 0/0:10:9,1,0,0 0/1:26:20,2,3,1
11 4976768 rs112749434_4976768 C T . PASS SOMATIC;SNP;AF=0.01,0.11;MQ=48;DB;1000G GT:DP:DP4 0/0:119:48,70,1,0 0/0:133:40,79,13,1
11 46685523 . G T . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:24:22,2,0,0 0/0:50:39,5,6,0
11 62491813 . A G . PASS SOMATIC;SNP;AF=0.00,0.26;MQ=60 GT:DP:DP4 0/0:132:93,39,0,0 0/1:129:75,21,28,5
11 67066621 . T G . PASS SOMATIC;SNP;AF=0.02,0.10;MQ=60 GT:DP:DP4 0/0:42:13,28,0,1 0/0:59:15,38,0,6
11 67141168 . T G . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:49:16,32,0,0 0/0:52:11,36,1,4
11 89880616 . G A . DPHIGH SOMATIC;SNP;AF=0.00,0.23;MQ=60 GT:DP:DP4 0/0:335:149,186,0,0 0/1:310:121,118,30,41
11 118771237 . G T . PASS SOMATIC;SNP;AF=0.00,0.45;MQ=60 GT:DP:DP4 0/0:6:5,1,0,0 0/1:20:8,3,8,1
11 118972250 . G A . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:130:79,51,0,0 0/0:134:86,33,11,4
11 128709601 . C T . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:198:93,105,0,0 0/1:212:92,76,20,24
12 7593650 . C A . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=60 GT:DP:DP4 0/0:108:84,24,0,0 0/1:133:100,6,23,4
12 15637123 . G A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:285:147,137,1,0 0/1:325:158,98,36,33
12 40838348 . G A . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:59:21,38,0,0 0/1:97:19,58,8,12
12 48736803 . C T . PASS SOMATIC;SNP;AF=0.00,0.22;MQ=60 GT:DP:DP4 0/0:110:76,34,0,0 0/1:106:69,14,19,4
12 58005815 . C G . PASS SOMATIC;SNP;AF=0.01,0.12;MQ=60 GT:DP:DP4 0/0:80:25,53,0,1 0/0:57:21,29,1,6
12 118519876 . T A . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=59 GT:DP:DP4 0/0:41:40,1,0,0 0/0:78:70,0,8,0
12 123744955 rs1980251_123744955 G A . PASS SOMATIC;SNP;AF=0.00,0.55;MQ=60;DB;1000G GT:DP:DP4 0/0:10:6,4,0,0 0/1:11:2,3,4,2
13 46559647 . C T . PASS SOMATIC;SNP;AF=0.00,0.08;MQ=60 GT:DP:DP4 0/0:189:100,89,0,0 0/0:181:112,55,10,4
13 75873491 . T C . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=60 GT:DP:DP4 0/0:39:31,8,0,0 0/1:41:29,1,10,1
13 114240096 . A T . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:115:104,11,0,0 0/0:139:129,3,6,1
14 24592052 . G C . PASS SOMATIC;SNP;AF=0.00,0.25;MQ=60 GT:DP:DP4 0/0:16:16,0,0,0 0/1:32:24,0,8,0
14 56106079 rs202151780_56106079 G T . PASS SOMATIC;SNP;AF=0.02,0.17;MQ=60;DB GT:DP:DP4 0/0:43:3,39,0,1 0/0:53:3,41,0,9
14 56111007 . A T . PASS SOMATIC;SNP;AF=0.00,0.17;MQ=60 GT:DP:DP4 0/0:48:45,3,0,0 0/1:81:63,4,14,0
14 56111273 . T A . PASS SOMATIC;SNP;AF=0.02,0.10;MQ=60 GT:DP:DP4 0/0:41:1,39,0,1 0/0:58:1,51,0,6
14 73535090 . A T . PASS SOMATIC;SNP;AF=0.02,0.11;MQ=60 GT:DP:DP4 0/0:50:14,35,0,1 0/0:72:20,44,0,8
15 31117403 rs798127_31117403 T C . PASS SOMATIC;SNP;AF=0.00,0.41;MQ=60;DB;1000G GT:DP:DP4 0/0:10:3,7,0,0 0/1:17:7,3,2,5
15 60257271 . C G . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60 GT:DP:DP4 0/0:39:8,31,0,0 0/1:48:7,34,1,6
15 102306446 . C T . PASS SOMATIC;SNP;AF=0.00,0.64;MQ=60 GT:DP:DP4 0/0:7:2,5,0,0 0/1:11:1,3,3,4
16 721394 . A G . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=59 GT:DP:DP4 0/0:25:1,23,0,0 0/0:53:2,44,0,7
16 723647 rs1045716_723647 C G . PASS SOMATIC;SNP;AF=0.00,0.61;MQ=60;DB;1000G GT:DP:DP4 0/0:10:4,6,0,0 0/1:18:3,4,0,11
16 830926 rs3765332_830926 A G . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60;DB GT:DP:DP4 0/0:129:63,66,0,0 0/0:181:96,75,4,6
16 1252381 . G A . PASS SOMATIC;SNP;AF=0.00,0.22;MQ=60 GT:DP:DP4 0/0:79:46,33,0,0 0/1:113:68,20,16,9
16 2098051 . G A . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=60 GT:DP:DP4 0/0:22:6,16,0,0 0/1:55:15,29,3,8
16 2499034 . T C . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:79:46,32,0,0 0/0:102:58,39,2,3
16 22260277 . A T . PASS SOMATIC;SNP;AF=0.02,0.15;MQ=60 GT:DP:DP4 0/0:44:9,34,0,1 0/0:48:4,37,0,7
16 24185995 . G A . PASS SOMATIC;SNP;AF=0.00,0.22;MQ=60 GT:DP:DP4 0/0:96:8,88,0,0 0/1:130:16,85,3,26
16 46533905 . T C . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:42:32,10,0,0 0/1:65:47,6,9,3
16 56916199 . G A . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:49:48,1,0,0 0/1:85:70,0,14,1
16 58555118 . C A . PASS SOMATIC;SNP;AF=0.00,0.08;MQ=60 GT:DP:DP4 0/0:158:65,93,0,0 0/0:195:79,100,6,10
16 67919619 . T C . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:21:12,9,0,0 0/0:47:29,12,6,0
17 1679912 . G A . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:137:81,56,0,0 0/0:133:94,33,5,1
17 7978925 rs397514532_7978925 G A . PASS SOMATIC;SNP;AF=0.00,0.15;MQ=60;DB GT:DP:DP4 0/0:35:27,8,0,0 0/1:40:27,7,6,0
17 48941378 . T A . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:25:0,25,0,0 0/0:60:0,52,0,8
17 48941388 . G C . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:17:0,17,0,0 0/0:51:0,45,0,6
17 71382643 . T C . PASS SOMATIC;SNP;AF=0.00,0.17;MQ=60 GT:DP:DP4 0/0:80:42,38,0,0 0/1:77:41,23,9,4
17 74134279 . T G . PASS SOMATIC;SNP;AF=0.00,0.21;MQ=60 GT:DP:DP4 0/0:28:2,26,0,0 0/1:38:4,26,0,8
17 81082390 rs368105194_81082390 T C . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=53;DB GT:DP:DP4 0/0:12:6,6,0,0 0/1:19:10,2,2,5
17 81082391 . G A . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=53 GT:DP:DP4 0/0:12:6,6,0,0 0/1:19:10,2,2,5
19 37310275 . T A . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:57:31,26,0,0 0/1:78:37,31,6,4
19 47996115 . A G . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:55:40,15,0,0 0/0:90:67,18,1,4
19 49464493 . A C . PASS SOMATIC;SNP;AF=0.00,0.16;MQ=60 GT:DP:DP4 0/0:47:1,46,0,0 0/0:63:1,52,0,10
20 2736269 . G A . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:51:47,4,0,0 0/0:54:43,5,5,1
20 3297522 . T C . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:36:0,36,0,0 0/0:66:2,57,0,7
20 17639941 rs13036886_17639941 A C . PASS SOMATIC;SNP;AF=0.01,0.07;MQ=56;DB GT:DP:DP4 0/0:89:47,40,1,0 0/0:103:64,32,6,1
21 43938612 . G T . PASS SOMATIC;SNP;AF=0.00,0.16;MQ=60 GT:DP:DP4 0/0:109:46,63,0,0 0/1:106:32,57,6,11
22 23615369 . C T . PASS SOMATIC;SNP;AF=0.00,0.18;MQ=60 GT:DP:DP4 0/0:51:25,26,0,0 0/1:84:42,27,7,8
22 29688538 rs370548139_29688538 T C . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60;DB GT:DP:DP4 0/0:51:45,6,0,0 0/1:66:53,6,5,2
22 40755448 . A T . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=59 GT:DP:DP4 0/0:22:0,22,0,0 0/0:51:0,45,0,6
22 44892786 . G T . PASS SOMATIC;SNP;AF=0.00,0.20;MQ=60 GT:DP:DP4 0/0:70:47,23,0,0 0/1:92:51,23,16,2
vcf2maf_cluster/raw_vcf/I002_001.stdzd.vcf 0000644 0001750 0001750 00000046644 14431663311 020635 0 ustar lucianhu lucianhu ##fileformat=VCFv4.1
##fileDate=20210510
##pancancerversion=1.0
##reference=<ID=hs37d5,Source=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz>;
##center="DKFZ"
##workflowName=DKFZ_SNV_workflow
##workflowVersion=1.0.0
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=GERMLINE,Number=0,Type=Flag,Description="Indicates if record is a germline mutation">
##INFO=<ID=UNCLEAR,Number=0,Type=Flag,Description="Indicates if the somatic status of a mutation is unclear">
##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, INS or DEL">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency in primary data, for each ALT allele, in the same order as listed">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="RMS Mapping Quality">
##INFO=<ID=1000G,Number=0,Type=Flag,Description="Indicates membership in 1000Genomes">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position in the sample">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases">
##FILTER=<ID=RE,Description="variant in UCSC_27Sept2013_RepeatMasker.bed.gz region and/or SimpleTandemRepeats_chr.bed.gz region, downloaded from UCSC genome browser and/or variant in segmental duplication region, annotated by annovar">
##FILTER=<ID=BL,Description="variant in DAC-Blacklist from ENCODE or in DUKE_EXCLUDED list, both downloaded from UCSC genome browser">
##FILTER=<ID=DP,Description="<= 5 reads total at position in tumor">
##FILTER=<ID=SB,Description="Strand bias of reads with mutant allele = zero reads on one strand">
##FILTER=<ID=TAC,Description="less than 6 reads in Tumor at position">
##FILTER=<ID=dbSNP,Description="variant in dbSNP135">
##FILTER=<ID=DB,Description="variant in 1000Genomes, ALL.wgs.phase1_integrated_calls.20101123.snps_chr.vcf.gz or dbSNP">
##FILTER=<ID=HSDEPTH,Description="variant in HiSeqDepthTop10Pct_chr.bed.gz region, downloaded from UCSC genome browser">
##FILTER=<ID=MAP,Description="variant overlaps a region from wgEncodeCrgMapabilityAlign100mer.bedGraph.gz:::--breakPointMode --aEndOffset=1 with a value below 0.5, punishment increases with a decreasing mapability">
##FILTER=<ID=SBAF,Description="Strand bias of reads with mutant allele = zero reads on one strand and variant allele frequency below 0.1">
##FILTER=<ID=FRQ,Description="variant allele frequency below 0.05">
##FILTER=<ID=TAR,Description="Only one alternative read in Tumor at position">
##FILTER=<ID=UNCLEAR,Description="Classification is unclear">
##FILTER=<ID=DPHIGH,Description="Too many reads mapped in control at this region">
##FILTER=<ID=DPLOWC,Description="Only 5 or less reads in control">
##FILTER=<ID=1PS,Description="Only two alternative reads, one on each strand">
##FILTER=<ID=ALTC,Description="Alternative reads in control">
##FILTER=<ID=ALTCFR,Description="Alternative reads in control and tumor allele frequency below 0.3">
##FILTER=<ID=FRC,Description="Variant allele frequency below 0.3 in germline call">
##FILTER=<ID=YALT,Description="Variant on Y chromosome with low allele frequency">
##FILTER=<ID=VAF,Description="Variant allele frequency in tumor < 5 times allele frequency in control">
##FILTER=<ID=BI,Description="Bias towards a PCR strand or sequencing strand">
##SAMPLE=<ID=CONTROL,SampleName=control_NA,Individual=NA,Description="Control">
##SAMPLE=<ID=TUMOR,SampleName=tumor_NA,Individual=NA,Description="Tumor">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CONTROL TUMOR
1 16380108 . C T . RE;DPHIGH SOMATIC;SNP;AF=0.00,0.46;MQ=60 GT:DP:DP4 0/0:492:310,180,1,1 0/1:522:213,69,169,71
1 16875489 rs525286_16875489 G A . PASS SOMATIC;SNP;AF=0.02,0.14;MQ=49;DB GT:DP:DP4 0/0:50:1,48,0,1 0/1:69:3,56,1,9
1 35163879 . C T . PASS SOMATIC;SNP;AF=0.00,0.57;MQ=60 GT:DP:DP4 0/0:6:4,2,0,0 0/1:7:2,1,3,1
1 38018326 . T G . DPHIGH SOMATIC;SNP;AF=0.00,0.45;MQ=60 GT:DP:DP4 0/0:485:232,253,0,0 0/1:583:150,171,131,131
1 49118939 . G A . PASS SOMATIC;SNP;AF=0.01,0.52;MQ=60 GT:DP:DP4 0/0:94:80,13,1,0 0/1:111:49,4,56,2
1 67885903 . G C . DPHIGH SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:378:112,266,0,0 0/0:370:107,244,4,15
1 82220167 . C G . PASS SOMATIC;SNP;AF=0.00,0.31;MQ=60 GT:DP:DP4 0/0:17:9,8,0,0 0/1:16:6,5,2,3
1 111150195 rs75308045_111150195 A G . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60;DB;1000G GT:DP:DP4 0/0:13:7,6,0,0 0/1:10:3,2,4,1
1 119134914 rs1911176_119134914 T C . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60;DB;1000G GT:DP:DP4 0/0:12:6,6,0,0 0/1:8:3,2,2,1
1 153903460 . A T . DPHIGH SOMATIC;SNP;AF=0.00,0.39;MQ=60 GT:DP:DP4 0/0:347:150,197,0,0 0/1:444:121,148,83,92
1 227967938 rs10916207_227967938 G A . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60;DB;1000G GT:DP:DP4 0/0:12:11,1,0,0 0/1:14:8,0,5,1
2 37036113 . G A . DPHIGH SOMATIC;SNP;AF=0.00,0.39;MQ=60 GT:DP:DP4 0/0:385:138,247,0,0 0/1:448:86,187,59,116
2 37036114 . C A . DPHIGH SOMATIC;SNP;AF=0.00,0.39;MQ=60 GT:DP:DP4 0/0:385:137,247,1,0 0/1:451:88,188,59,116
2 58311963 . C T . PASS SOMATIC;SNP;AF=0.03,0.41;MQ=60 GT:DP:DP4 0/0:34:32,1,1,0 0/1:56:30,3,22,1
2 71297507 . T G . PASS SOMATIC;SNP;AF=0.00,0.23;MQ=58 GT:DP:DP4 0/0:11:10,1,0,0 0/0:26:20,0,6,0
2 171243615 . G C . DPHIGH SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:348:262,86,0,0 0/0:426:355,45,24,2
2 219894180 . T C . PASS SOMATIC;SNP;AF=0.00,0.40;MQ=60 GT:DP:DP4 0/0:281:246,35,0,0 0/1:486:270,20,185,11
2 222428960 . A C . DPHIGH SOMATIC;SNP;AF=0.00,0.39;MQ=60 GT:DP:DP4 0/0:533:230,302,0,0 0/1:590:169,189,119,113
2 242515306 rs12623749_242515306 G A . PASS SOMATIC;SNP;AF=0.00,0.60;MQ=60;DB;1000G GT:DP:DP4 0/0:10:8,2,0,0 0/1:10:2,2,4,2
3 7721792 . G A . PASS SOMATIC;SNP;AF=0.00,0.83;MQ=60 GT:DP:DP4 0/0:290:175,115,0,0 0/1:163:21,6,101,35
3 15521034 . C T . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:15:2,13,0,0 0/1:25:1,21,1,2
3 46307009 . G C . DPHIGH SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:478:190,288,0,0 0/0:384:135,210,14,25
3 111671794 rs17492619_111671794 G A . PASS SOMATIC;SNP;AF=0.00,0.73;MQ=60;DB;1000G GT:DP:DP4 0/0:12:4,8,0,0 0/1:11:0,3,1,7
3 117716258 . C A . PASS SOMATIC;SNP;AF=0.00,0.44;MQ=60 GT:DP:DP4 0/0:11:3,8,0,0 0/1:16:1,8,1,6
3 130650718 . G C . PASS SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:20:19,1,0,0 0/1:19:11,0,7,1
3 158323011 . G A . DPHIGH SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:340:49,291,0,0 0/0:375:45,307,3,20
3 171394562 rs200078686_171394562 G A . PASS SOMATIC;SNP;AF=0.00,0.49;MQ=60;DB;1000G GT:DP:DP4 0/0:221:97,124,0,0 0/1:200:63,39,52,46
3 194174701 . T G . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:30:4,26,0,0 0/0:62:2,53,0,7
4 10027605 . G A . PASS SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:252:97,153,0,1 0/1:253:72,76,39,66
4 35508027 rs61795985_35508027 A C . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60;DB;1000G GT:DP:DP4 0/0:10:4,6,0,0 0/1:14:4,4,5,1
4 84376532 . G C . DPHIGH SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:767:354,411,1,1 0/1:979:282,287,210,200
4 106919227 . C G . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60 GT:DP:DP4 0/0:8:5,3,0,0 0/1:8:5,0,1,2
4 126371299 . T A . DPHIGH SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:570:406,164,0,0 0/1:685:316,81,235,53
4 126371300 . A G . DPHIGH SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:577:409,168,0,0 0/1:687:317,82,235,53
5 2896292 . C T . PASS SOMATIC;SNP;AF=0.00,0.56;MQ=60 GT:DP:DP4 0/0:8:5,3,0,0 0/1:9:4,0,3,2
5 10308182 rs77385368_10308182 C A . PASS SOMATIC;SNP;AF=0.00,0.25;MQ=60;DB;1000G GT:DP:DP4 0/0:11:4,7,0,0 0/1:12:3,6,2,1
5 12512778 . T G . PASS SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:11:3,8,0,0 0/1:19:6,5,4,4
5 14912109 . C T . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=60 GT:DP:DP4 0/0:17:4,13,0,0 0/1:11:1,7,1,2
5 60188635 . C T . PASS SOMATIC;SNP;AF=0.00,0.46;MQ=60 GT:DP:DP4 0/0:59:37,22,0,0 0/1:92:23,27,23,19
5 118971396 . G A . DPHIGH SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:320:122,198,0,0 0/1:352:68,135,57,92
5 127607713 . G T . PASS SOMATIC;SNP;AF=0.00,0.34;MQ=60 GT:DP:DP4 0/0:186:126,60,0,0 0/1:218:112,31,50,25
5 131308764 . C A . PASS SOMATIC;SNP;AF=0.00,0.28;MQ=60 GT:DP:DP4 0/0:15:4,11,0,0 0/1:32:5,18,5,4
6 7879352 . T G . PASS SOMATIC;SNP;AF=0.00,0.16;MQ=60 GT:DP:DP4 0/0:176:77,99,0,0 0/1:210:79,98,15,18
6 11185582 . C T . DPHIGH SOMATIC;SNP;AF=0.00,0.41;MQ=60 GT:DP:DP4 0/0:303:173,129,0,1 0/1:402:157,82,100,63
6 12749755 . A C . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:51:1,50,0,0 0/0:112:8,98,1,5
6 25279695 . A G . PASS SOMATIC;SNP;AF=0.00,0.60;MQ=60 GT:DP:DP4 0/0:10:5,5,0,0 0/1:10:3,1,2,4
6 32521413 . C G . PASS SOMATIC;SNP;AF=0.00,0.14;MQ=53 GT:DP:DP4 0/0:29:2,27,0,0 0/1:51:1,43,0,7
6 42146216 . C T . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:220:54,165,0,1 0/1:384:43,150,44,147
6 52134077 . C G . PASS SOMATIC;SNP;AF=0.00,0.40;MQ=60 GT:DP:DP4 0/0:124:38,86,0,0 0/1:150:19,71,15,45
6 103149963 . C T . PASS SOMATIC;SNP;AF=0.00,0.44;MQ=60 GT:DP:DP4 0/0:14:6,8,0,0 0/1:18:6,4,3,5
6 133782137 . G A . PASS SOMATIC;SNP;AF=0.00,0.41;MQ=60 GT:DP:DP4 0/0:79:79,0,0,0 0/1:137:81,0,56,0
7 72966829 . C T . PASS SOMATIC;SNP;AF=0.00,0.33;MQ=60 GT:DP:DP4 0/0:12:2,10,0,0 0/1:24:0,16,1,7
7 94517017 . C T . PASS SOMATIC;SNP;AF=0.00,0.54;MQ=60 GT:DP:DP4 0/0:6:4,2,0,0 0/1:13:4,2,4,3
7 98254195 . C T . DPHIGH SOMATIC;SNP;AF=0.00,0.45;MQ=60 GT:DP:DP4 0/0:343:266,76,1,0 0/1:446:212,33,172,29
7 98534894 . G A . PASS SOMATIC;SNP;AF=0.00,0.40;MQ=60 GT:DP:DP4 0/0:244:65,179,0,0 0/1:307:53,132,25,97
7 100074932 . T G . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:192:97,95,0,0 0/1:189:65,54,38,32
7 100780374 . G A . DPHIGH SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:1199:586,612,1,0 0/1:1556:544,353,389,270
7 107449913 . G A . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:25:11,14,0,0 0/1:30:11,8,2,9
7 119695271 . T C . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60 GT:DP:DP4 0/0:6:1,5,0,0 0/1:14:3,5,1,5
7 120690943 . G A . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:104:71,33,0,0 0/1:90:36,9,31,14
7 152797856 . G A . PASS SOMATIC;SNP;AF=0.00,0.67;MQ=60 GT:DP:DP4 0/0:12:8,4,0,0 0/1:12:4,0,7,1
7 153241794 . G A . PASS SOMATIC;SNP;AF=0.00,0.27;MQ=60 GT:DP:DP4 0/0:23:7,16,0,0 0/1:30:7,15,2,6
8 17541691 rs2410501_17541691 G A . PASS SOMATIC;SNP;AF=0.00,0.79;MQ=60;DB;1000G GT:DP:DP4 0/0:11:10,1,0,0 0/1:14:3,0,10,1
8 35624775 . C T . PASS SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:12:0,12,0,0 0/1:24:0,14,2,8
8 38271168 . T C . PASS SOMATIC;SNP;AF=0.00,0.44;MQ=59 GT:DP:DP4 0/0:79:65,14,0,0 0/1:147:74,8,57,8
8 68292046 . C T . PASS SOMATIC;SNP;AF=0.00,0.57;MQ=60 GT:DP:DP4 0/0:13:6,7,0,0 0/1:7:1,2,2,2
8 94935299 . G T . DPHIGH SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:427:234,193,0,0 0/0:492:301,166,14,11
8 124810436 . C T . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:287:218,69,0,0 0/1:276:117,20,126,13
8 133185028 . G C . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:40:0,40,0,0 0/0:78:0,70,0,8
9 30689616 . C A . PASS SOMATIC;SNP;AF=0.00,0.11;MQ=60 GT:DP:DP4 0/0:107:34,73,0,0 0/0:171:45,107,7,12
9 100894452 rs2231662_100894452 G A . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=60;DB;1000G GT:DP:DP4 0/0:177:83,94,0,0 0/0:233:127,86,14,6
9 116859336 . C G . PASS SOMATIC;SNP;AF=0.00,0.34;MQ=60 GT:DP:DP4 0/0:14:13,1,0,0 0/1:35:23,0,11,1
9 119662922 . T C . PASS SOMATIC;SNP;AF=0.00,0.67;MQ=60 GT:DP:DP4 0/0:6:5,1,0,0 0/1:6:2,0,3,1
9 128827725 rs62567582_128827725 A G . PASS SOMATIC;SNP;AF=0.00,0.60;MQ=60;DB;1000G GT:DP:DP4 0/0:11:7,4,0,0 0/1:10:3,1,5,1
9 131396138 . G A . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:235:139,96,0,0 0/0:254:170,72,9,3
9 136029671 . C T . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:179:51,128,0,0 0/1:232:37,109,23,63
10 22006549 . T C . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=58 GT:DP:DP4 0/0:28:21,7,0,0 0/1:30:12,3,12,3
10 30722914 . G C . PASS SOMATIC;SNP;AF=0.00,0.57;MQ=60 GT:DP:DP4 0/0:6:2,4,0,0 0/1:7:3,0,1,3
10 75611090 rs2688626_75611090 G A . PASS SOMATIC;SNP;AF=0.00,0.33;MQ=60;DB;1000G GT:DP:DP4 0/0:11:6,5,0,0 0/1:15:8,2,3,2
10 84625070 . G T . DPHIGH SOMATIC;SNP;AF=0.00,0.38;MQ=60 GT:DP:DP4 0/0:485:346,139,0,0 0/1:476:245,48,148,35
10 86008933 . C T . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:10:0,10,0,0 0/1:19:2,10,2,5
10 88418474 . G T . PASS SOMATIC;SNP;AF=0.00,0.10;MQ=60 GT:DP:DP4 0/0:78:6,72,0,0 0/0:175:7,150,0,18
11 15262028 . T C . DPHIGH SOMATIC;SNP;AF=0.00,0.43;MQ=60 GT:DP:DP4 0/0:318:213,105,0,0 0/1:388:162,61,130,35
11 68924646 . C T . PASS SOMATIC;SNP;AF=0.00,0.25;MQ=60 GT:DP:DP4 0/0:9:6,3,0,0 0/1:12:8,1,1,2
11 80666846 . C T . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:14:6,8,0,0 0/1:22:6,5,8,3
11 85636415 rs113614037_85636415 T C . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60;DB;1000G GT:DP:DP4 0/0:10:5,5,0,0 0/1:16:3,7,3,3
12 9226961 rs1805661_9226961 G A . PASS SOMATIC;SNP;AF=0.00,0.69;MQ=60;DB;1000G GT:DP:DP4 0/0:10:8,2,0,0 0/1:16:5,0,11,0
12 48789095 . G A . PASS SOMATIC;SNP;AF=0.00,0.57;MQ=60 GT:DP:DP4 0/0:9:3,6,0,0 0/1:7:1,2,2,2
12 81593586 . A G . DPHIGH SOMATIC;SNP;AF=0.00,0.40;MQ=60 GT:DP:DP4 0/0:394:118,276,0,0 0/1:396:78,158,52,108
12 119778334 rs12314123_119778334 C A . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60;DB;1000G GT:DP:DP4 0/0:10:6,4,0,0 0/1:7:2,2,1,2
12 122186239 . C G . PASS SOMATIC;SNP;AF=0.00,0.51;MQ=60 GT:DP:DP4 0/0:142:97,45,0,0 0/1:177:71,16,80,10
13 24408169 rs9507169_24408169 C T . PASS SOMATIC;SNP;AF=0.00,0.42;MQ=60;DB;1000G GT:DP:DP4 0/0:11:5,6,0,0 0/1:12:5,2,1,4
13 110777408 rs75329905_110777408 G A . PASS SOMATIC;SNP;AF=0.00,0.56;MQ=60;DB;1000G GT:DP:DP4 0/0:10:5,5,0,0 0/1:9:2,2,3,2
13 111137401 . G T . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:97:11,86,0,0 0/0:137:27,102,1,7
14 21510975 rs1952526_21510975 G T . PASS SOMATIC;SNP;AF=0.00,0.62;MQ=60;DB;1000G GT:DP:DP4 0/0:11:8,3,0,0 0/1:16:6,0,8,2
14 39762729 . C T . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60 GT:DP:DP4 0/0:47:1,46,0,0 0/1:88:0,50,0,38
14 42882306 . C T . RE;DPHIGH SOMATIC;SNP;AF=0.01,0.46;MQ=60 GT:DP:DP4 0/0:158:118,38,1,1 0/1:159:73,13,69,4
14 65253578 . C T . DPHIGH SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:557:272,283,0,2 0/1:573:181,179,105,108
14 83040731 rs2022647_83040731 G A . PASS SOMATIC;SNP;AF=0.00,0.44;MQ=60;DB;1000G GT:DP:DP4 0/0:15:4,11,0,0 0/1:16:6,3,3,4
15 66273135 . G T . PASS SOMATIC;SNP;AF=0.00,0.37;MQ=60 GT:DP:DP4 0/0:119:62,57,0,0 0/1:139:49,38,28,24
15 69687485 . G A . PASS SOMATIC;SNP;AF=0.00,0.69;MQ=60 GT:DP:DP4 0/0:15:5,10,0,0 0/1:13:2,2,3,6
15 75765923 . G A . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:89:76,13,0,0 0/1:118:57,2,53,6
15 83520381 rs3784376_83520381 G A . PASS SOMATIC;SNP;AF=0.00,0.42;MQ=60;DB;1000G GT:DP:DP4 0/0:11:7,4,0,0 0/1:12:3,4,3,2
15 90015033 rs2072692_90015033 A G . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60;DB;1000G GT:DP:DP4 0/0:10:5,5,0,0 0/1:8:3,2,1,2
16 4248009 . C T . PASS SOMATIC;SNP;AF=0.01,0.45;MQ=60 GT:DP:DP4 0/0:99:6,92,0,1 0/1:127:3,67,3,54
16 7500801 . C T . PASS SOMATIC;SNP;AF=0.00,0.71;MQ=60 GT:DP:DP4 0/0:9:4,5,0,0 0/1:7:1,1,4,1
16 52060364 . T C . PASS SOMATIC;SNP;AF=0.00,0.13;MQ=60 GT:DP:DP4 0/0:89:37,52,0,0 0/1:68:23,36,3,6
16 58283811 . C T . PASS SOMATIC;SNP;AF=0.00,0.33;MQ=60 GT:DP:DP4 0/0:54:49,5,0,0 0/1:130:85,2,41,2
16 65016133 . C T . PASS SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:291:163,128,0,0 0/0:346:223,105,14,4
17 6380434 . G T . PASS SOMATIC;SNP;AF=0.00,0.38;MQ=60 GT:DP:DP4 0/0:245:147,98,0,0 0/1:335:153,55,87,40
17 7311973 . C T . PASS SOMATIC;SNP;AF=0.00,0.48;MQ=60 GT:DP:DP4 0/0:283:153,130,0,0 0/1:294:104,49,72,69
17 20602285 . G C . PASS SOMATIC;SNP;AF=0.00,0.09;MQ=53 GT:DP:DP4 0/0:90:17,73,0,0 0/0:81:14,60,2,5
17 29206419 rs72811661_29206419 T G . PASS SOMATIC;SNP;AF=0.00,0.41;MQ=60;DB;1000G GT:DP:DP4 0/0:260:197,63,0,0 0/1:253:133,16,96,8
17 47874119 . T C . PASS SOMATIC;SNP;AF=0.00,0.40;MQ=60 GT:DP:DP4 0/0:73:61,12,0,0 0/1:95:45,12,33,5
17 74977456 . C G . PASS SOMATIC;SNP;AF=0.00,0.71;MQ=60 GT:DP:DP4 0/0:8:5,3,0,0 0/1:7:1,1,4,1
17 80107679 . G A . PASS SOMATIC;SNP;AF=0.00,0.12;MQ=60 GT:DP:DP4 0/0:51:26,25,0,0 0/0:64:30,26,6,2
17 80941924 rs62076012_80941924 G A . PASS SOMATIC;SNP;AF=0.00,0.64;MQ=60;DB GT:DP:DP4 0/0:15:5,10,0,0 0/1:11:4,0,2,5
17 80941993 rs72490492_80941993 T C . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=59;DB GT:DP:DP4 0/0:11:6,5,0,0 0/1:14:5,2,3,4
18 9344927 . A T . PASS SOMATIC;SNP;AF=0.00,0.54;MQ=60 GT:DP:DP4 0/0:7:4,3,0,0 0/1:13:6,0,6,1
18 19182537 . T G . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:12:8,4,0,0 0/1:12:6,0,6,0
19 680506 . T A . PASS SOMATIC;SNP;AF=0.00,0.48;MQ=60 GT:DP:DP4 0/0:23:5,18,0,0 0/1:31:4,12,4,11
19 2191685 rs34982309_2191685 G A . PASS SOMATIC;SNP;AF=0.00,0.62;MQ=60;DB;1000G GT:DP:DP4 0/0:10:6,4,0,0 0/1:8:2,1,3,2
19 4443035 . C G . PASS SOMATIC;SNP;AF=0.00,0.44;MQ=60 GT:DP:DP4 0/0:294:184,109,0,1 0/1:319:146,34,102,37
19 6469052 rs34064666_6469052 T G . RE;DPHIGH SOMATIC;SNP;AF=0.00,0.46;MQ=60;DB GT:DP:DP4 0/0:233:66,166,0,1 0/1:291:42,116,44,89
19 6736113 . G A . PASS SOMATIC;SNP;AF=0.00,0.40;MQ=60 GT:DP:DP4 0/0:75:17,58,0,0 0/1:87:6,46,8,27
19 7976053 . G A . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:134:30,104,0,0 0/0:250:49,186,4,11
19 8201205 . G A . PASS SOMATIC;SNP;AF=0.00,0.06;MQ=60 GT:DP:DP4 0/0:245:86,159,0,0 0/0:357:136,199,11,11
19 10824391 . C G . PASS SOMATIC;SNP;AF=0.00,0.42;MQ=60 GT:DP:DP4 0/0:69:11,58,0,0 0/1:123:18,53,11,41
19 51129043 rs12985643_51129043 A G . PASS SOMATIC;SNP;AF=0.00,0.69;MQ=52;DB;1000G GT:DP:DP4 0/0:28:22,5,0,0 0/1:13:4,0,6,3
19 56113787 . G T . PASS SOMATIC;SNP;AF=0.00,0.41;MQ=60 GT:DP:DP4 0/0:129:74,55,0,0 0/1:179:76,30,43,30
19 56114056 . C T . PASS SOMATIC;SNP;AF=0.00,0.44;MQ=60 GT:DP:DP4 0/0:185:108,77,0,0 0/1:244:88,48,65,43
20 2688636 . G A . DPHIGH SOMATIC;SNP;AF=0.00,0.43;MQ=60 GT:DP:DP4 0/0:593:339,252,1,1 0/1:557:200,120,156,81
20 4004729 . A G . PASS SOMATIC;SNP;AF=0.01,0.05;MQ=57 GT:DP:DP4 0/0:98:64,33,1,0 0/0:132:89,36,3,4
20 31608305 . G A . DPHIGH SOMATIC;SNP;AF=0.00,0.43;MQ=60 GT:DP:DP4 0/0:402:217,185,0,0 0/1:499:175,109,125,90
20 32645903 . G A . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:7:2,5,0,0 0/1:8:1,3,3,1
20 35322203 . G C . PASS SOMATIC;SNP;AF=0.00,0.56;MQ=60 GT:DP:DP4 0/0:14:4,10,0,0 0/1:16:1,6,2,7
20 45092609 . C T . PASS SOMATIC;SNP;AF=0.00,0.50;MQ=60 GT:DP:DP4 0/0:28:27,1,0,0 0/1:42:21,0,21,0
20 56131175 . C G . DPHIGH SOMATIC;SNP;AF=0.00,0.05;MQ=60 GT:DP:DP4 0/0:498:326,172,0,0 0/0:550:390,134,20,6
21 26734168 . C T . PASS SOMATIC;SNP;AF=0.00,0.47;MQ=59 GT:DP:DP4 0/0:95:51,44,0,0 0/1:120:43,21,38,18
21 38243210 rs3827188_38243210 C G . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60;DB;1000G GT:DP:DP4 0/0:10:7,3,0,0 0/1:7:2,2,2,1
21 38630122 . C A . PASS SOMATIC;SNP;AF=0.00,0.62;MQ=60 GT:DP:DP4 0/0:9:3,6,0,0 0/1:13:2,3,3,5
21 40935544 . G A . PASS SOMATIC;SNP;AF=0.00,0.47;MQ=60 GT:DP:DP4 0/0:8:3,5,0,0 0/1:15:2,6,1,6
22 43784506 rs56319817_43784506 G C . PASS SOMATIC;SNP;AF=0.00,0.44;MQ=60;DB;1000G GT:DP:DP4 0/0:10:8,2,0,0 0/1:9:3,2,3,1
22 50221748 . G C . PASS SOMATIC;SNP;AF=0.00,0.67;MQ=60 GT:DP:DP4 0/0:7:5,2,0,0 0/1:9:2,1,5,1
X 347300 . C G . PASS SOMATIC;SNP;AF=0.00,0.43;MQ=60 GT:DP:DP4 0/0:58:29,29,0,0 0/1:54:12,19,16,7
X 2445607 . C A . PASS SOMATIC;SNP;AF=0.00,0.75;MQ=60 GT:DP:DP4 0/0:8:3,5,0,0 0/1:8:2,0,1,5
X 22603340 . G T . PASS SOMATIC;SNP;AF=0.00,0.75;MQ=60 GT:DP:DP4 0/0:10:3,7,0,0 0/1:12:0,3,2,7
X 47498718 . C T . PASS SOMATIC;SNP;AF=0.00,0.45;MQ=60 GT:DP:DP4 0/0:55:10,45,0,0 0/1:97:5,48,7,37
X 48371015 . A C . DPHIGH SOMATIC;SNP;AF=0.00,0.35;MQ=60 GT:DP:DP4 0/0:454:317,137,0,0 0/1:536:271,76,144,45
X 69647035 . G A . DPHIGH SOMATIC;SNP;AF=0.00,0.45;MQ=60 GT:DP:DP4 0/0:769:344,423,2,0 0/1:841:243,223,198,177
X 111625006 . G C . RE;DPHIGH SOMATIC;SNP;AF=0.00,0.45;MQ=52 GT:DP:DP4 0/0:286:84,202,0,0 0/1:358:61,135,53,109
X 112357396 rs141091049_112357396 A G . PASS SOMATIC;SNP;AF=0.00,0.46;MQ=53;DB;1000G GT:DP:DP4 0/0:12:7,5,0,0 0/1:13:6,1,5,1
vcf2maf_cluster/validate_vcf2maf_2023.py 0000664 0001750 0001750 00000010164 14434175164 020577 0 ustar lucianhu lucianhu #!/usr/bin/env python3
import glob
import argparse
import os
import re
import datetime
# This function examines the information in the MAF and VCF file formats and looks for conflicts or missing data.
def compare_vcf2maf(invcffile, maffile):
comparing = "Comparing {} and {}".format(os.path.basename(invcffile),os.path.basename(maffile))
invcf={}
invcfcount = 0
with open(invcffile, "r") as fh:
for line in fh:
if line.startswith("##"):
continue
elif line.startswith("#CHROM"):
headers = line.split()
continue
else:
invcfcount += 1
linedata = line.split()
invcf["{}-{}".format(linedata[0], linedata[1])] = dict(zip(headers,linedata))
# print(invcf["{}-{}".format(linedata[0], linedata[1])])
maf={}
with open(maffile, "r") as fh:
for line in fh:
if line.startswith("#"):
continue
elif line.startswith("Hugo_Symbol"):
headers = line.split()
else:
linedata = line.split()
maf["{}-{}".format(linedata[4], linedata[5])] = dict(zip(headers,linedata))
# print(maf["{}-{}".format(linedata[4], linedata[5])])
result = []
for k,d in invcf.items():
if k not in maf.keys():
result.append("CHROM-LOC '{}' missing in maf".format(k))
continue
if invcf[k]["REF"] != maf[k]["Reference_Allele"]:
result.append("({}) REF MISMATCH (vcf)'{}' v (maf)'{}'".format(
k, invcf[k]["REF"], maf[k]["Reference_Allele"] ))
continue
if invcf[k]["ALT"] != maf[k]["Tumor_Seq_Allele2"]:
result.append("({}) ALT MISMATCH (vcf)'{}' v (maf)'{}'".format(
k,invcf[k]["ALT"],maf[k]["Tumor_Seq_Allele2"] ))
continue
if result == []:
result = "(OK) ({} variants)".format(invcfcount, comparing)
result = "{} {}".format(str(result), comparing)
return result
# Execute the main program
if __name__ == "__main__":
# Create an argument parser object
parser = argparse.ArgumentParser(description='Validation VCF input file to MAF output file.')
# Define a command-line argument
parser.add_argument('--datadir', action="store", dest = "datadir", required = True,
help = "Folder containing both of the input-output data. ")
parser.add_argument('--vcfdir', action="store", dest = "vcfdir", required = True,
help = "Folder containing the VCF files.")
parser.add_argument('--mafdir', action="store", dest = "mafdir", required = True,
help = "Folder containing the MAT files.")
# Parse the arguments and retrieve as a dictionary
args = vars(parser.parse_args())
# Get the current date
current_date = datetime.datetime.now().strftime("%d-%m-%Y")
# Define the output file name with the current date
output_file = "{}/validate_vcf2maf_{}.out".format(args["datadir"], current_date)
# Redirect the output to the file
with open(output_file, "w") as f:
for vcfpath in glob.iglob(os.path.join(args["vcfdir"], "*.stdzd.vcf")):
vcffile = os.path.basename(vcfpath) # Extract PID from the vcfpath
PID = vcffile.split(".")[0]
expected_vep_vcf = f"{PID}.stdzd.vep.vcf"
if expected_vep_vcf not in os.listdir(args["vcfdir"]):
f.write("(VEP missing) Output VEP file for VCF infile '{}' does not exist! vcf2maf appears to encounter a VEP annotation error.\n".format(vcffile))
maffile = vcffile.replace(".stdzd.vcf", ".maf")
mafpath = os.path.join(args["mafdir"], maffile)
if not os.path.isfile(mafpath):
f.write("(MAF missing) Output MAF file for VCF infile '{}' does not exist! vcf2maf appears to have failed.\n".format(vcffile))
continue
# Call the compare function
result = compare_vcf2maf(vcfpath, mafpath)
f.write(result + '\n')