Question: How to filter variant calls based on specific reference and alternate allele frequency ratio during variations calling?
0
gravatar for bioinfo89
10 months ago by
bioinfo8940
bioinfo8940 wrote:

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!

snp vcf • 458 views
ADD COMMENTlink modified 10 months ago by finswimmer11k • written 10 months ago by bioinfo8940

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

ADD REPLYlink written 10 months ago by finswimmer11k

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

ADD REPLYlink written 10 months ago by bioinfo8940
0
gravatar for Nandini
10 months ago by
Nandini780
London
Nandini780 wrote:

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

ADD COMMENTlink written 10 months ago by Nandini780

Hi Nandini,

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

Thanks!

ADD REPLYlink written 10 months ago by bioinfo8940
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