Entering edit mode
16 months ago
tanbiswas6
▴
10
I'm using vcf2maf to convert my PASSED variants VCF file (generated using GATK-Mutect2 pipeline followed by VEP annotation). I have run the following command and getting the following errors at every position. Can anyone suggest what I should do? Here's my command and errors:
iit@iit:~$ perl /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl --input-vcf P01.filtered.PASS.vep.vcf --output-maf /P01.filtered.PASS.maf --tumor-id P01-TD normal-id P01-BD --ref-fasta /home/iit/GRCh38_full_analysis_set_plus_decoy_hla.fa
Argument "chr1:158611393-158611591" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 44.
Argument "chr1:158611393-158611591" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 45.
Argument "chr1:158611393-158611591" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 46.
Argument "chr1:158611393-158611591" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 47.
Argument "chr1:158611393-158611591" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 48.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 71.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 72.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 73.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 74.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 75.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 76.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 77.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 78.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 79.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 80.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 81.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 82.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 83.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 84.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 85.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 86.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 87.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 88.
Argument "chr11:840268" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 89.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 90.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 91.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 92.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 93.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 94.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 95.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 96.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 97.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 98.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 99.
Argument "chr14:21511310" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 100.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 101.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 102.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 103.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 104.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 105.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 106.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 107.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 108.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 109.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 110.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 111.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 112.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 113.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 114.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 115.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 116.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 117.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 118.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 119.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 120.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 121.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 122.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 123.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 124.
Argument "chr14:105490995" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 125.
Argument "chr14:106235321-106235322" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 126.
Argument "chr14:106235327" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 127.
Argument "chr16:29554500" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 128.
Argument "chr16:29554502" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 129.
Argument "chr16:85112441" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 130.
Argument "chr16:85112441" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 131.
Argument "chr16:85112441" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 132.
Argument "chr16:85112443" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 133.
Argument "chr16:85112443" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 134.
Argument "chr16:85112443" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 135.
Argument "chr19:38229676" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 136.
Argument "chr19:38229676" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 137.
Argument "chr19:38229676" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 138.
Argument "chr19:38229676" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 139.
Argument "chr19:38229676" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 140.
Argument "chr19:38229676" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 141.
Argument "chr19:38229676" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 142.
Argument "chr19:38229678-38229679" isn't numeric in subtraction (-) at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 382, <GEN2> line 143.
[W::fai_get_val] Reference chr11_840268_C/T:-1-15 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr11_840268_C/T:-1-15
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. at /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/vcf2maf-1.6.21/vcf2maf.pl line 410.
Please suggest what should I do.
Thank you
Regards,
Tanay
your file is not a VCF. The first tab delimited column should be something like "chr1" but it founds a whole string like " chr11_840268_C/T:-1-15"