How to distinguish homozygous Reference with Missing genotype after merging multiple

jdpr_100

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#1

How to distinguish homozygous Reference with Missing genotype after merging multiple

07-03-2016, 06:47 PM

The SNPs were called for each individual and multiple VCF files were combined. Is it a way to find out missing genotypes and checks if it is homozygous Reference or no-called site after merging multiple VCF files?
Thanks in advance for your help.

Last edited by jdpr_100; 07-03-2016, 06:52 PM.
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dickie_ho

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Join Date: Mar 2013

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#2

07-04-2016, 04:04 AM

Hey mate

Check this out https://github.com/lindenb/jvarkit/w...ssingGenotypes

haven't used it yet myself, just regenerating all my bam files again because I ran into the same issue

Cheers

Josh
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How to distinguish homozygous Reference with Missing genotype after merging multiple

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