Question: Extracting imputation (INFO) quality scores for specific SNPs from VCF files
0
gravatar for e.jabbari
2.4 years ago by
e.jabbari0
e.jabbari0 wrote:

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!?

genotype imputation • 1.8k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by e.jabbari0
1
gravatar for Pierre Lindenbaum
2.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Pierre Lindenbaum129k
0
gravatar for e.jabbari
2.4 years ago by
e.jabbari0
e.jabbari0 wrote:

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.

ADD COMMENTlink written 2.4 years ago by e.jabbari0
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