Filter VCF file for variant alleles
Hello everyone,
I am looking to filter my VCF file with multiple samples to keep those variants that vary with respect to the reference (i.e., not 0/0) in more than x samples. For example, if x is 10, I want to only keep SNPs that vary in more than 5 samples in my dataset. Thanks in advance
• 1,410 views
•
link
updated
by
Ram
•
written
by
miguellarrazlopezdenovales •
•
written
by
miguellarrazlopezdenovales •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Help with Finding SNPs in H. pylori Assembled Genomes
written by vrao •
-
Using COUNT with bcftools filter
written by mykle hoban •
-
Problem in merging multiple samples VCF file obtained from Structural variant caller Lumpy
written by sardana.thakur.prachi •
-
Compare VCFs against background frequencies
written by miguellarrazlopezdenovales •
-
Filter vcf file based on the GTs of a single sample
written by miguellarrazlopezdenovales •
-
Filter vaiants having no AF information
written by waqaskhokhar999
-
finding out SNPs from SNVs and breed specific SNPs
written by prasundutta87
-
Code to select randomly 1 SNP per scaffold
written by angelaparody •
-
supertranscripts (conceptual question)
written by paraskevopou •
-
How to find variants that are common in one population but rare in others (population differentiati…
written by SOHAIL
What have you tried? You've mentioned bcftools as a tag, have you read the manual?
I've tried bcftools, which seems to be the closest I've got, but I can't find anything to do this. I have also found vcftools --max-non-ref-ac, which I think might be able to do this, but I am not really sure how to use it, and was wondering if anyone has any experience here. Thanks
It's in there. If you had looked a little deeper, you would have found - on your own - exactly what Pierre has pointed to below.
use a filtering expression https://samtools.github.io/bcftools/bcftools.html#expressions , something like;