The current GATK version is 3.7-0
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Ratio of reads

Member
edited January 2013

Hi all,
I am working with GATK on illumina data that was created from yeasts (SK1 strain). Since it is sequencing of a colony and not the exact same organism, I am using a filter that I wrote on the ratio of the reads that support the alternative allele. Is anyone else using something similar? Is there a build-in filter like that?

Post edited by Geraldine_VdAuwera on
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Comments

• Charlestown, MAMember

You mean you're filtering out all reads that do not have the alternate allele?

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