How to filter variant calls based on specific reference and alternate allele frequency ratio during variations calling?

Question

[bioinfo89]

Hi All,

I have been working on targeted amplicon sequencing data (>200 samples). I use GATK for variant calling. So my question is, is there a parameter in variant calling where we can specify to not call variants if the reference allele frequency is say >0.8 than the alternate allele frequency?

I ask this because I am getting few SNPs which are called in >20 samples, one of which is pathogenic according to ClinVar but it does not get validated using Sanger sequencing. So I checked its allele frequency ratio and it shows that reference and alternate allele frequencies do not have much of a difference (eg. for a SNP at position 43082434 at chr17, the ref allele depth is 2716 while alternate allele depth is 1162 hence the frequencies are 0.7 and 0.29 respectively). I want to remove such calls from the variant calling.

Can anyone suggest something on this?

Thanks!

[finswimmer]

Hello,

do you have all samples in one vcf or one vcf per sample?

In general for filtering vcf based on several criteria one can use bcftools view or SnpSift.

fin swimmer

[bioinfo89]

I have one vcf per sample! Thanks I will try this!

Answer 1

[NB]

You can use GATK's SelectVariants to filter variants of interest based in several criteria

[bioinfo89]

Hi Nandini,

Could you suggest what parameter to take using select variants which would help to achieve what I want?

Thanks!