This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Calculate GQ for samples VCF

I have received a VCF from a collaborator. I would like to filter SNP's with the GQ values of the samples. However, this is not present in the FORMAT field of the VCF that I received. Is there a way to calculate or add the GQ values to each sample for each SNP of the vcf that I am working with? Here are the variables that I have for my samples in the format field:

GT:DP:RO:QR:AO:QA:GL

freebayes linux vcf gatk
• 1,557 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by timothy.delory • timothy.delory 
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genot$
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##FORMAT=<ID=MIN,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">

The GQ is present in the header, but the samples do not have this measure.

• 0 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by timothy.delory • timothy.delory

0 answers

No answers yet.

Log in to answer this question.

More posts like this