Question: vcf filtration for homozygous calls
gravatar for nikhilachowdary1999
7 months ago by
nikhilachowdary19990 wrote:

Freebayes has called some records with the GT = 1/1 tag, even if there are non-zero values for RO, SRF and SRR. We want to filter and retain only those records that show = > 90% alternate allele frequency. Is there any tool which can help in doing this?

srr gt srf ao vcf • 166 views
ADD COMMENTlink written 7 months ago by nikhilachowdary19990

Take a look at BCFtools view and filter

ADD REPLYlink written 7 months ago by Kevin Blighe49k
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