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Filtering vcf on per sample AD and PL

Member Posts: 43

Hello,

I would like to filter my multi-sample vcf using per sample metrics such as AD and PL. However, these are provided as comma-separated lists of numbers. Does anyone know how I can filter, for example, on PL of 0/1 genotype in sample A?

Best wishes,

Kath

Tagged:

Hi Kath,

Yes you can; have a look at this document to get you started: http://www.broadinstitute.org/gatk/guide/article?id=51

Geraldine Van der Auwera, PhD

• Member Posts: 43

Thanks Geraldine, that works great!

• PortugalMember Posts: 1

Hello! The link that you provided is now broken. Where did it direct to? I'm trying to understand how I can filter on the PL field. Thanks!

• EdinburghMember Posts: 2

Hi,

As far as I know, there are no resources available for applying VQSR to vcf files of chicken, so I have to use Hard Filtering to filter my snps of chicken. I read the general recommendation for hard-filtering, which is very helpful. To be more confident on my snps, I would like to determine these parameters by myself. Which GATK tools can help me generate the density plots for each filter parameter?

Cheers

Zejun