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Analyzing sample dataset

Using reads around the PTEN tumor suppresor gene locus (chr10:87,863,113-87,971,930 on GRCh38), the sample dataset was prepared by GATK Best Practice for RNA-Seq. The dataset contains the BAM and VCF files (not FASTQ)

To download:

curl -LO https://zenodo.org/record/6109305/files/sampledataset.tar.gz
tar -zxf sampledataset.tar.gz

RNAIndel integrates the callset from the built-in caller and that from GAKT (pre-called).
To do this, input the original BAM file (i.e., sample.bam, not the pre-processed one) and the GATK VCF file:

rnaindel PredictIndels -i sampledataset/sample.bam \ # do not use sample.gatk.bam
                       -o test.vcf \
                       -r sampledataset/chr10.fa \
                       -d data_dir_grch38 \
                       -v sampledataset/sample.gatk.vcf.gz \

The output VCF reports the expressed coding indels called from the 2 methods. Each indel is annoated in INFO field for prdicted class (somatic, germline, artifact) and by which caller it was detected (built-in, external, both). In this example, indels predicted as somatic are:

CHROM   POS         REF  ALT        INFO
chr10   87957917    AC   GGCCCATGG  predicted_class=somatic;...;CALLER=both
chr10   87957955    C    CCTGGGTT   predicted_class=somatic;...;CALLER=both

These PTEN indels are called by the built-in and GATK HaplotypeCaller. The first indel is reported as a complex indel AC>GGCCCATGG.