Question: Multiple VCF filtering
0
gravatar for deniselavezzari
6 weeks ago by
deniselavezzari0 wrote:

Hi!

I have a vcf with 20 samples and I want to remove from it the variants that are commons (with the same zygosity) to all samples. How can I do it?

Thanks

illumina exom wgs vcf • 87 views
ADD COMMENTlink modified 6 weeks ago by RamRS28k • written 6 weeks ago by deniselavezzari0
2
gravatar for RamRS
6 weeks ago by
RamRS28k
Houston, TX
RamRS28k wrote:

Use bcftools view with an exclude/include expression that operates on COUNT(GT="hom") as shown in the examples here: https://samtools.github.io/bcftools/bcftools.html#expressions

ADD COMMENTlink written 6 weeks ago by RamRS28k

Thank you very much.

ADD REPLYlink written 6 weeks ago by deniselavezzari0

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.

Upvote|Bookmark|Accept

ADD REPLYlink written 6 weeks ago by RamRS28k
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