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VCF files-Keep all alternative alleles

Hello

I have VCF outputs of Mutect2 (GATK4) with no downsampling. Some variants have multiple calls, which are comma separated in ALT column. I would like to preserve all of them before inputting in VEP including their respective TLOD and AF scores into a new VCF file where each alternative allele is in one separate line.

Here is an example:

original VCF file:

chr1 149813407 . G A,T . . DP=17510;ECNT=9;POP_AF=5.000e-08,5.000e-08;TLOD=4.36,49.82 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1/2:15000,22,59:0.049,0.051:7274,4,30:7726,18,29:32,33:149,153,144:48,45:13,7:0.010,0.010,3.912e-03:1.000,1.055e-10,3.564e-06

New VCF file:

chr1 149813407 . G A . . DP=17510;ECNT=9;POP_AF=5.000e-08;TLOD=4.36 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1/2:15000,22,59:0.049,0.051:7274,4,30:7726,18,29:32,33:149,153,144:48,45:13,7:0.010,0.010,3.912e-03:1.000,1.055e-10,3.564e-06

chr1 149813407 . G T . . DP=17510;ECNT=9;POP_AF=5.000e-08;TLOD=49.82 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1/2:15000,22,59:0.049,0.051:7274,4,30:7726,18,29:32,33:149,153,144:48,45:13,7:0.010,0.010,3.912e-03:1.000,1.055e-10,3.564e-06

I am very new in VCF processing but I have looked at bcftools and vcftools to no avail. I appreciate your help

Thank you

snp bcftools vcf vcftools samtools
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by juara • juara

@OP: . There are tools to do that. I tested on VEP offline and current version doesn't support splitting of alt allele records in VCF output with default parameters VCF as output.

• 1 views • link
written by cpad0112 cpad0112

Yes I tried that too. The bcftools comment works though! Thanks

• 1 views • link
written by juara • juara

1 answer

https://samtools.github.io/bcftools/bcftools.html

bcftools norm [OPTIONS] file.vcf.gz ", split multiallelic sites into multiple rows"

 -m, --multiallelics -|+[snps|indels|both|any]
    split multiallelic sites into biallelic records (-) or join biallelic sites into multiallelic records (+). An optional type string can follow which controls variant types which should be split or merged together: If only SNP records should be split or merged, specify snps; if both SNPs and indels should be merged separately into two records, specify both; if SNPs and indels should be merged into a single record, specify any.
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you very much for your comment. this works like charm! :) I am just wondering, whether there is a function in bcftools that I can merge FORMAT field data to INFO field with?

• 1 views • link
written by juara • juara

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