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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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Empty 't_depth' 't_ref_count' 't_alt_count' #332

Open QingruXu44004 opened 2 years ago

QingruXu44004 commented 2 years ago

Hi，

This is my sample vcf file:

chrM 593 . T C . PASS AS_FilterStatus=SITE;AS_SB_TABLE=1,0|172,137;DP=317;ECNT=3;MBQ=30,25;MFRL=220,155;MMQ=60,60;MPOS=27;OCM=0;POPAF=2.40;TLOD=883.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:1,309:0.992:310:1,85:0,91:1,247:1,0,172,137 chrM 625 . G A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=225,176|2,2;DP=420;ECNT=3;MBQ=18,20;MFRL=147,137;MMQ=60,60;MPOS=34;OCM=0;POPAF=2.40;TLOD=1.43 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:401,4:9.722e-03:405:7,0:6,1:311,2:225,176,2,2 chrM 750 . A G . PASS AS_FilterStatus=SITE;AS_SB_TABLE=0,1|154,189;DP=358;ECNT=3;MBQ=19,23;MFRL=180,149;MMQ=60,60;MPOS=21;OCM=0;POPAF=2.40;TLOD=957.80 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:1,343:0.996:344:0,94:0,97:0,265:0,1,154,189 chrM 1438 . A G . PASS AS_FilterStatus=SITE;AS_SB_TABLE=0,0|103,103;DP=208;ECNT=4;MBQ=0,20;MFRL=0,147;MMQ=60,60;MPOS=23;OCM=0;POPAF=2.40;TLOD=609.64 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,206:0.994:206:0,46:0,69:0,159:0,0,103,103 chrM 2110 . A G . PASS AS_FilterStatus=SITE;AS_SB_TABLE=115,108|1,2;DP=237;ECNT=3;MBQ=20,20;MFRL=141,119;MMQ=60,60;MPOS=25;OCM=0;POPAF=2.40;TLOD=1.74 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:223,3:0.017:226:77,1:66,0:165,2:115,108,1,2 chrM 2472 . A G . PASS AS_FilterStatus=SITE;AS_SB_TABLE=89,77|1,1;DP=176;ECNT=3;MBQ=28,28;MFRL=146,89;MMQ=60,60;MPOS=9;OCM=0;POPAF=2.40;TLOD=2.24 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:166,2:0.014:168:55,1:63,0:137,1:89,77,1,1 chrM 2877 . C T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=91,80|1,1;DP=180;ECNT=2;MBQ=20,29;MFRL=145,95;MMQ=60,60;MPOS=7;OCM=0;POPAF=2.40;TLOD=2.45 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:171,2:0.016:173:45,0:45,1:125,1:91,80,1,1 chrM 3010 . G A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=0,0|109,58;DP=175;ECNT=4;MBQ=0,31;MFRL=0,147;MMQ=60,60;MPOS=24;OCM=0;POPAF=2.40;TLOD=541.07 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,167:0.993:167:0,54:0,72:1,147:0,0,109,58 chrM 3078 . C T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=92,113|1,2;DP=215;ECNT=4;MBQ=18,20;MFRL=149,135;MMQ=60,60;MPOS=37;OCM=0;POPAF=2.40;TLOD=2.61 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:205,3:0.019:208:42,1:48,0:159,2:92,113,1,2 chrM 3231 . T C . PASS AS_FilterStatus=SITE;AS_SB_TABLE=101,103|2,2;DP=212;ECNT=2;MBQ=20,20;MFRL=144,113;MMQ=60,60;MPOS=16;OCM=0;POPAF=2.40;TLOD=3.55 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:204,4:0.019:208:59,1:64,1:155,2:0|1:3231_T_C:3231:101,103,2,2

This is the command that I ran:

perl vcf2maf.pl --input-vcf test.vcf --output-maf test.maf --tumor-id my_sample_ID --ref-fasta Homo_sapiens_assembly38.chrM.fasta --vep-path ensembl-vep-release-106 --vep-data ensembl-vep-release-106/.vep/ --filter-vcf ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz --ncbi-build GRCh38

The output file has 't_depth', 't_ref_count', 't_alt_count' columns but are all empty. Could you help me look at why this content is missing? I feel like it is a parsing vcf file problem. Thanks!

ckandoth commented 2 years ago

Your VCF looks fine. But make sure that "tumor-id" exactly matches the name of the sample ID in your VCF column header for th genotype field. This is needed to extract the AD field which contains this data.