Extracting imputation (INFO) quality scores for specific SNPs from VCF files

Question

[e.jabbari]

Would be very grateful for help.

I have a VCF.gz file for imputed SNP data. I know for a fact that this file contains imputation (INFO) quality scores as in a subsequent QC step I've used bcftools to only keep SNPs with an INFO score >0.70 bcftools view -Ou -i 'INFO>0.7'

However, I am struggling to understand how to view the actual INFO score for an individual SNP from the VCF.gz file.

Any ideas!?

Answer 1

[Pierre Lindenbaum]

I am struggling to understand how to view the actual INFO score for an individual SNP

try to use

bcftools query

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

Answer 2

[e.jabbari]

Thanks for replying Pierre. Unfortunately I've already tried to find the solution in the manual but have had no luck. Thanks for your time.