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Multiple alleles (say G->A/C) at same position, no depth info in VCF

Hello,

Sorry for the simplistic question, but I am new at this.

Using Mutect2 (and a few other callers) to look for somatic variants, we are getting multiple cases where several alt alleles are identified at the same position (on same single line in VCF).

When we try extracting info from VCF (through Gemini database), we can't get any additional info for those variants with multiple alt alleles at same position. In the VCF, I can't see any allele depth.

Why are we getting a single entry for both alt alleles ? How can we correct our VCF so we can see how many reads we have for each alt allele at this same position ? Sorry, I'm just running out of time to solve it. Let me know where I can find info on this.

Thanks, Charles

next-gen alignment genome software error
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updated by Kevin Blighe Kevin Blighe • written by charles.meuniercm • charles.meuniercm

show us one line of with this multiple ALT, including the #CHROM header pelase.

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

In these situations, it is good practice to split these multi-allelic calls into multiple lines. You can use the following code:

bcftools norm -Ov -m-any MyFile.vcf > MyFile.Split.vcf

Also get into the habit of checking your ref alleles against an existing reference genome (this also left-aligns indels):

bcftools norm -m-any MyFile.vcf | bcftools norm -Ov --check-ref w -f /ReferenceMaterial/1000Genomes/human_g1k_v37.fasta > MyFile.Split.RefCheck.vcf
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written by Kevin Blighe Kevin Blighe

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