wjaratlerdsiri
commented
8 years ago Now work now. I have changed to the following:
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reference=file:///project/RDS-SMS-PCaGenomes-RW/weejar/Homo_sapiens_assembly38_omosome.fasta
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR
1 285442 . G A . PASS SOMATIC TD 53,9 1 736683 . A G . PASS SOMATIC TD 79,6 1 757769 . AAAT A . PASS SOMATIC TD 90,5 1 801412 . C A . PASS SOMATIC TD 68,9 1 988912 . A G . PASS SOMATIC TD 62,12 1 1065263 . C G . PASS SOMATIC TD 6,8
Dear Author,
Now GATK uses Mutec2 for somatic SNV&INDEL calls (https://software.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php)
Is it possible if adding support for Mutec2 vcf files in create_phylowgs_inputs.py?
Thankyou for your time in making this great program available. This will help my research in prostate cancer.
james
Below is sample data: **## fileformat=VCFv4.2
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SAMPLE=<ID=NORMAL,SampleName=UP2
SAMPLE=<ID=TUMOR,SampleName=UP
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reference=file:/Homo_sapiens_assembly38_chromosome.fasta
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL**
chr1 20686501 . TACAC T . PASS ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=2.62;RPA=8,6;RU=AC;STR;TLOD=6.35 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:13,4:0.111:0:4:.:56,114:2:0 0/0:8,0:0.071:0:0:.:0,0:0:0 chr1 20817233 . G A . PASS ECNT=1;HCNT=8;MAX_ED=.;MIN_ED=.;NLOD=3.31;TLOD=24.07 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:7,9:0.563:5:4:0.556:179,250:4:3 0/0:12,0:0.00:0:0:.:319,0:7:5 chr1 21091401 . T A . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=10.39;TLOD=79.36 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:34,31:0.484:20:11:0.645:925,852:18:16 0/0:37,0:0.00:0:0:.:931,0:15:22 chr1 21103954 . G GAC . PASS ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=10.24;RPA=1,2;RU=AC;STR;TLOD=91.90 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:44,26:0.377:13:13:.:1257,743:20:24 0/0:34,0:0.00:0:0:.:912,0:17:17 chr1 21418556 . A G . PASS ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=6.32;TLOD=12.09 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:42,7:0.143:2:5:0.714:1171,172:22:20 0/0:21,0:0.00:0:0:.:564,0:7:14 chr1 21610165 . G A . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=9.53;TLOD=99.01 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:51,40:0.449:19:21:0.475:1322,1085:27:24 0/0:32,0:0.00:0:0:.:780,0:11:21 chr1 21746746 . T A . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=11.13;TLOD=93.16 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:44,37:0.449:16:21:0.432:1213,1062:23:21 0/0:38,0:0.00:0:0:.:1039,0:18:20