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Old 05-01-2019, 09:35 AM   #8
questor2010
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Location: Seattle, WA

Join Date: Mar 2010
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Quote:
Originally Posted by XeroxHero69 View Post
Thanks for your reply. Could you give me an example of the format of what a command that would use bcftools view to find a base at a position would look like?
Sure - here's an example:

bcftools view -f PASS --threads 8 -T target.bed -o gnomad.genomes.r2.1.sites.target.vcf.gz -O z gnomad.genomes.r2.1.sites.vcf.bgz

In this case, I'm using a bed file, instead of a single region. It is pulling out the FILTER=PASS variants that intersect the bed file into a new compressed vcf file. The source vcf file in this case is 465GB. If you have a single variant, you could use -t 1:11022. It might be best to specify a short range (1:11015-11030) if you're looking at indels - variant callers represent indels in different ways and you want to be sure you properly intersect them.
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