Update/metafusion

CHANGELOG.md

@@ -10,12 +10,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#117](https://github.com/mskcc/forte/pull/117) - add supporting-reads_gene-fusions\*.zip files to fusioncatcher outputs
 
 - [#118](https://github.com/mskcc/forte/pull/118) - change the way the plug-n-play starfusion reference is downloaded.
+- -[#126](https://github.com/mskcc/forte/pull/126) - enable clinical genes prioritization in Metafusion
 
 ### `Fixed`
 
 - [#119](https://github.com/mskcc/forte/pull/119) - change script error behavior in METAFUSION_RUN process
 
 - [#125](https://github.com/mskcc/forte/pull/125) - update upload-artifact version because the version previously in use (v2) is deprecated.
+- [#126](https://github.com/mskcc/forte/pull/126) - 0 based gene bed annotation with removal of incomplete transcripts
 
 ### `Dependencies`
 

assets/clinical_allowlist_hg19.txt

@@ -0,0 +1,319 @@
+gene_name ensembl_transcript refseq_transcript
+AR ENST00000374690 NM_000044
+BTK ENST00000308731 NM_000061
+CDKN2A ENST00000304494 NM_000077
+EPOR ENST00000222139 NM_000121
+ESR1 ENST00000206249 NM_000125
+FGFR2 ENST00000358487 NM_000141
+FGFR3 ENST00000440486 NM_000142
+JAK3 ENST00000458235 NM_000215
+KIT ENST00000288135 NM_000222
+MET ENST00000397752 NM_000245
+PTCH1 ENST00000331920 NM_000264
+NME1 ENST00000393196 NM_000269
+RAG1 ENST00000299440 NM_000448
+GNAS ENST00000371085 NM_000516
+RAG2 ENST00000311485 NM_000536
+CD44 ENST00000428726 NM_000610
+CD79B ENST00000006750 NM_000626
+BCL2 ENST00000333681 NM_000633
+CSF1 ENST00000329608 NM_000757
+DCK ENST00000286648 NM_000788
+PGR ENST00000325455 NM_000926
+RARA ENST00000254066 NM_000964
+SS18 ENST00000415083 NM_001007559
+MYBL1 ENST00000522677 NM_001080416
+NUTM2A ENST00000381707 NM_001099338
+BCOR ENST00000378444 NM_001123385
+YAP1 ENST00000282441 NM_001130145
+MYB ENST00000341911 NM_001130173
+BIRC3 ENST00000263464 NM_001165
+MEAF6 ENST00000296214 NM_001270875
+NUTM2B ENST00000429828 NM_001278495
+EIF4A1 ENST00000293831 NM_001416
+ID4 ENST00000378700 NM_001546
+ACVR2A ENST00000241416 NM_001616
+ARAF ENST00000377045 NM_001654
+RHOA ENST00000418115 NM_001664
+BCL6 ENST00000406870 NM_001706
+BMP7 ENST00000395863 NM_001719
+CCND2 ENST00000261254 NM_001759
+CCND3 ENST00000372991 NM_001760
+ENTPD1 ENST00000371205 NM_001776
+CDC25A ENST00000302506 NM_001789
+CEBPE ENST00000206513 NM_001805
+CEBPG ENST00000284000 NM_001806
+ERBB3 ENST00000267101 NM_001982
+ETV6 ENST00000396373 NM_001987
+FOXO1 ENST00000379561 NM_002015
+FLT1 ENST00000282397 NM_002019
+GATA1 ENST00000376670 NM_002049
+IRF8 ENST00000268638 NM_002163
+IDH2 ENST00000330062 NM_002168
+IL7R ENST00000303115 NM_002185
+ITPKB ENST00000429204 NM_002221
+JAK1 ENST00000342505 NM_002227
+LMO1 ENST00000335790 NM_002315
+LTK ENST00000263800 NM_002344
+MAL ENST00000309988 NM_002371
+MN1 ENST00000302326 NM_002430
+IRF4 ENST00000380956 NM_002460
+MYH11 ENST00000300036 NM_002474
+NPM1 ENST00000296930 NM_002520
+NRAS ENST00000369535 NM_002524
+NTRK1 ENST00000524377 NM_002529
+PBX1 ENST00000420696 NM_002585
+PDGFB ENST00000331163 NM_002608
+PDGFRB ENST00000261799 NM_002609
+PIM1 ENST00000373509 NM_002648
+PLAG1 ENST00000316981 NM_002655
+PPAT ENST00000264220 NM_002703
+PRKACA ENST00000308677 NM_002730
+PRKAR2B ENST00000265717 NM_002736
+PRKCA ENST00000413366 NM_002737
+PRKD1 ENST00000331968 NM_002742
+MAP2K1 ENST00000307102 NM_002755
+PTPN1 ENST00000371621 NM_002827
+PTPN11 ENST00000351677 NM_002834
+RAF1 ENST00000251849 NM_002880
+SOX11 ENST00000322002 NM_003108
+SRF ENST00000265354 NM_003131
+STAT6 ENST00000300134 NM_003153
+TCF3 ENST00000262965 NM_003200
+TNFSF4 ENST00000281834 NM_003326
+TYK2 ENST00000525621 NM_003331
+XPO1 ENST00000401558 NM_003400
+HMGA2 ENST00000403681 NM_003483
+TP63 ENST00000264731 NM_003722
+RAB7L1 ENST00000367139 NM_003929
+NFKB1 ENST00000226574 NM_003998
+BCL2A1 ENST00000267953 NM_004049
+DNTT ENST00000371174 NM_004088
+E2F2 ENST00000361729 NM_004091
+FLT3 ENST00000241453 NM_004119
+ALK ENST00000389048 NM_004304
+BCR ENST00000305877 NM_004327
+CALR ENST00000316448 NM_004343
+CEBPA ENST00000498907 NM_004364
+CREBBP ENST00000262367 NM_004380
+ERBB2 ENST00000269571 NM_004448
+ETV5 ENST00000306376 NM_004454
+EZH2 ENST00000320356 NM_004456
+SH3BP5 ENST00000383791 NM_004844
+NRG2 ENST00000361474 NM_004883
+CDKN2B ENST00000276925 NM_004936
+ETV1 ENST00000430479 NM_004956
+FUS ENST00000254108 NM_004960
+JAK2 ENST00000381652 NM_004972
+KRAS ENST00000311936 NM_004985
+PDCD1 ENST00000334409 NM_005018
+NUP214 ENST00000359428 NM_005085
+ABL1 ENST00000318560 NM_005157
+BCL3 ENST00000164227 NM_005178
+CBL ENST00000264033 NM_005188
+CEBPD ENST00000408965 NM_005195
+EGFR ENST00000275493 NM_005228
+ERBB4 ENST00000342788 NM_005235
+EWSR1 ENST00000397938 NM_005243
+FGR ENST00000374005 NM_005248
+FOS ENST00000303562 NM_005252
+GLI1 ENST00000228682 NM_005269
+GRB7 ENST00000309156 NM_005310
+MPL ENST00000372470 NM_005373
+SH2B3 ENST00000341259 NM_005475
+TLX1 ENST00000370196 NM_005521
+LMO2 ENST00000257818 NM_005574
+LYL1 ENST00000264824 NM_005583
+MUSK ENST00000374448 NM_005592
+TMPRSS2 ENST00000332149 NM_005656
+PRKD3 ENST00000234179 NM_005813
+IDH1 ENST00000345146 NM_005896
+IKZF1 ENST00000331340 NM_006060
+TFG ENST00000240851 NM_006070
+DNAJB1 ENST00000254322 NM_006145
+NFE2L2 ENST00000397062 NM_006164
+NTRK2 ENST00000277120 NM_006180
+PDGFRA ENST00000257290 NM_006206
+PIK3CA ENST00000263967 NM_006218
+TFE3 ENST00000315869 NM_006521
+NCOA2 ENST00000452400 NM_006540
+FOSB ENST00000353609 NM_006732
+U2AF1 ENST00000291552 NM_006758
+YWHAE ENST00000264335 NM_006761
+KAT6A ENST00000265713 NM_006766
+PIM2 ENST00000376509 NM_006875
+DNMT3B ENST00000328111 NM_006892
+PYCR1 ENST00000329875 NM_006907
+PICALM ENST00000393346 NM_007166
+BRD3 ENST00000303407 NM_007371
+CHIC2 ENST00000263921 NM_012110
+MGEA5 ENST00000361464 NM_012215
+NFATC2 ENST00000371564 NM_012340
+RLF ENST00000372771 NM_012421
+SF3B1 ENST00000335508 NM_012433
+STAT5B ENST00000293328 NM_012448
+TNFRSF13B ENST00000261652 NM_012452
+IKZF3 ENST00000346872 NM_012481
+FAM216A ENST00000377673 NM_013300
+BLNK ENST00000224337 NM_013314
+CD274 ENST00000381577 NM_014143
+SETD2 ENST00000409792 NM_014159
+LIMD1 ENST00000273317 NM_014240
+NEK6 ENST00000320246 NM_014397
+KIAA0101 ENST00000300035 NM_014736
+MAST1 ENST00000251472 NM_014975
+CAMTA1 ENST00000303635 NM_015215
+WWTR1 ENST00000360632 NM_015472
+VGLL3 ENST00000398399 NM_016206
+CYB5R2 ENST00000299498 NM_016229
+KLF2 ENST00000248071 NM_016270
+NUP98 ENST00000324932 NM_016320
+PAX5 ENST00000358127 NM_016734
+MBTD1 ENST00000586178 NM_017643
+EXOC2 ENST00000230449 NM_018303
+STRBP ENST00000348403 NM_018387
+PAG1 ENST00000220597 NM_018440
+BATF3 ENST00000243440 NM_018664
+MAML3 ENST00000509479 NM_018717
+AICDA ENST00000229335 NM_020661
+RET ENST00000355710 NM_020975
+LZTS1 ENST00000381569 NM_021020
+TLX3 ENST00000296921 NM_021025
+RELA ENST00000406246 NM_021975
+THADA ENST00000405975 NM_022065
+PRDM16 ENST00000270722 NM_022114
+RBM15 ENST00000369784 NM_022768
+CBFB ENST00000412916 NM_022845
+WHSC1L1 ENST00000317025 NM_023034
+FGFR1 ENST00000447712 NM_023110
+EBF1 ENST00000313708 NM_024007
+PHF1 ENST00000374516 NM_024165
+NOTCH2 ENST00000256646 NM_024408
+PDGFD ENST00000393158 NM_025208
+PDCD1LG2 ENST00000397747 NM_025239
+ZCCHC7 ENST00000336755 NM_032226
+CARD11 ENST00000396946 NM_032415
+MAML2 ENST00000524717 NM_032427
+GLIS2 ENST00000433375 NM_032575
+GATA2 ENST00000341105 NM_032638
+RSPO3 ENST00000356698 NM_032784
+CCNB3 ENST00000376042 NM_033031
+CCND1 ENST00000227507 NM_053056
+BCL11B ENST00000357195 NM_138576
+BAX ENST00000345358 NM_138761
+TAF15 ENST00000605844 NM_139215
+HOXA9 ENST00000343483 NM_152739
+PTK2B ENST00000346049 NM_173176
+JAZF1 ENST00000283928 NM_175061
+P2RY8 ENST00000381297 NM_178129
+RSPO2 ENST00000276659 NM_178565
+VGLL2 ENST00000326274 NM_182645
+PRKACB ENST00000370685 NM_182948
+CREB3L2 ENST00000330387 NM_194071
+TERT ENST00000310581 NM_198253
+SS18L1 ENST00000331758 NM_198935
+AKT1 ENST00000555528 NM_005163
+AR ENST00000396043 NM_001011645
+ARHGAP26 ENST00000274498 NM_015071
+BCORL1 ENST00000540052 NM_021946
+BRAF ENST00000288602 NM_004333
+BRD4 ENST00000263377 NM_058243
+CIC ENST00000575354 NM_015125
+CSF1 ENST00000369802 NM_172212
+DEK ENST00000397239 NM_003472
+EPC1 ENST00000263062 NM_025209
+ERG ENST00000417133 NM_004449
+ESR1 ENST00000440973 NM_001122742
+ETV4 ENST00000319349 NM_001986
+FGF1 ENST00000378046 NM_00800
+FGFR1 ENST00000397091 NM_015850
+FGFR4 ENST00000292408 NM_002011
+GRM1 ENST00000492807 NM_001278065
+IGF1R ENST00000268035 NM_000875
+LTK ENST00000453182 NM_001135685
+MKL2 ENST00000574045 NM_014048
+NCOA1 ENST00000288599 NM_147223
+NCOA3 ENST00000372004 NM_006534
+NOTCH1 ENST00000277541 NM_017617
+NR4A3 ENST00000330847 NM_173200
+NRG1 ENST00000522402 NM_001159996
+NRG1 ENST00000341377 NM_004495
+NRG1 ENST00000356819 NM_013956
+NRG1 ENST00000287842 NM_013957
+NRG1 ENST00000520502 NM_013959
+NRG1 ENST00000520407 NM_013962
+NTRK1 ENST00000392302 NM_001007792
+NTRK3 ENST00000317501 NM_001007156
+NTRK3 ENST00000317501 NM_002530
+NUTM1 ENST00000333756 NM_175741
+PAX3 ENST00000392069 NM_181459
+PAX7 ENST00000375375 NM_002584
+PPARG ENST00000287820 NM_015869
+PRB3 ENST00000381842 NM_006249
+PRKCB ENST00000303531 NM_002738
+PRKD2 ENST00000433867 NM_016457
+RAD51B ENST00000487270 NM_133509
+RET ENST00000340058 NM_020630
+ROS1 ENST00000368508 NM_002944
+SS18 ENST00000269137 NM_005637
+STAT6 ENST00000300134 NM_001178078
+TCF12 ENST00000438423 NM_207036
+TFEB ENST00000230323 NM_007162
+TMPRSS2 ENST00000398585 NM_001135099
+USP6 ENST00000574788 NM_004505
+AKT3 ENST00000366539 NM_005465
+ASXL1 ENST00000375687 NM_015338
+CCDC50 ENST00000392455 NM_174908
+CHD1 ENST00000284049 NM_001270
+CIITA ENST00000324288 NM_000246
+CRLF2 ENST00000400841 NM_022148
+CSF1R ENST00000286301 NM_005211
+CTLA4 ENST00000302823 NM_005214
+DLEU1 ENST00000378180 NR_002605
+FOXP1 ENST00000318789 NM_032682
+FUT8 ENST00000557164 NM_004480
+IL16 ENST00000394652 NM_004513
+KDM6A ENST00000377967 NM_021140
+LRMP ENST00000354454 NM_006152
+MALT1 ENST00000348428 NM_006785
+MECOM ENST00000494292 NM_004991
+MKL1 ENST00000355630 NM_020831
+MLF1 ENST00000355893 NM_022443
+MLLT4 ENST00000392108 NM_001040000
+MUC1 ENST00000337604 NM_002456
+MYC ENST00000377970 NM_002467
+MYD88 ENST00000396334 NM_002468
+NFKB2 ENST00000189444 NM_002502
+PLCG1 ENST00000244007 NM_002660
+PLCG2 ENST00000359376 NM_002661
+RANBP1 ENST00000331821 NM_002882
+RUNX1 ENST00000300305 NM_001754
+S1PR2 ENST00000590320 NM_004230
+SEMA6A ENST00000343348 NM_020796
+SERPINA9 ENST00000337425 NM_175739
+SETBP1 ENST00000282030 NM_015559
+TAL1 ENST00000371884 NM_003189
+WT1 ENST00000332351 NM_000378
+ABL2 ENST00000512653 NM_005158
+ASB13 ENST00000479033 NR_0024581
+BMF ENST00000354670 NM_033503
+CDK6 ENST00000265734 NM_001259
+CSF3R ENST00000373103 NM_156039
+DENND3 ENST00000519811 NM_014957
+DNM2 ENST00000389253 NM_004945
+DNMT3A ENST00000321117 NM_175629
+DUSP22 ENST00000344450 NM_020185
+FBXW7 ENST00000281708 NM_033632
+IKZF2 ENST00000457361 NM_016260
+KMT2A ENST00000534358 NM_005933
+MLLT10 ENST00000377072 NM_004641
+MME ENST00000460393 NM_000902
+NF1 ENST00000358273 NM_000267
+NT5C2 ENST00000343289 NM_012229
+PAICS ENST00000264221 NM_006452
+PHF6 ENST00000370800 NM_032335
+PML ENST00000395135 NM_002675
+SLC29A1 ENST00000427851 NM_001078175
+SRSF2 ENST00000359995 NM_003016
+STAT3 ENST00000404395 NM_003150
+STIL ENST00000360380 NM_003035

bin/Metafusion_forte.sh

@@ -7,15 +7,15 @@ set -eo pipefail
 # __author__ = "Alexandria Dymun"
 # __email__ = "[email protected]"
 # __contributor__ = "Anne Marie Noronha ([email protected])"
-# __version__ = "0.0.1"
+# __version__ = "0.0.2"
 # __status__ = "Dev"
 
 output_ANC_RT_SG=1
 RT_call_filter=1
 blck_filter=1
 ANC_filter=1
 usage() {
- echo "Usage: Metafusion_forte.sh --num_tools=<minNumToolsCalled> --genome_fasta <FASTA adds SEQ to fusion> --recurrent_bedpe <blacklistFusions> --outdir <outputDirectory> --cff <cffFile> --gene_bed <geneBedFile> --gene_info <geneInfoFile>" 1>&2;
+ echo "Usage: Metafusion_forte.sh --num_tools=<minNumToolsCalled> --genome_fasta <FASTA adds SEQ to fusion> --recurrent_bedpe <blacklistFusions> --outdir <outputDirectory> --cff <cffFile> --gene_bed <geneBedFile> --gene_info <geneInfoFile> --clinical_genes <clinicalGenes>" 1>&2;
  exit 1;
 }
 
@@ -50,6 +50,10 @@ while test $# -gt 0;do
  recurrent_bedpe="$2"
  shift 2
  ;;
+ --clinical_genes)
+ clinical_genes="$2"
+ shift 2
+ ;;
  *)
  #OTHER_ARGUMENTS+=("$1")
  shift # Remove generic argument from processing
@@ -83,10 +87,10 @@ cff=$outdir/$(basename $cff).renamed
 #Annotate cff
 if [ $genome_fasta ]; then
  echo Annotate cff, extract sequence surrounding breakpoint
- reann_cff_fusion.py --cff $cff --gene_bed $gene_bed --ref_fa $genome_fasta > $outdir/$(basename $cff).reann.WITH_SEQ
+ reann_cff_fusion.py --cff $cff --gene_bed $gene_bed --ref_fa $genome_fasta --clinical_genes $clinical_genes > $outdir/$(basename $cff).reann.WITH_SEQ
 else
  echo Annotate cff, no extraction of sequence surrounding breakpoint
- reann_cff_fusion.py --cff $cff --gene_bed $gene_bed > $outdir/$(basename $cff).reann.NO_SEQ
+ reann_cff_fusion.py --cff $cff --gene_bed $gene_bed --clinical_genes $clinical_genes > $outdir/$(basename $cff).reann.NO_SEQ
 fi
 
 # Assign .cff based on SEQ or NOSEQ