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Created 2012-08-12 14:29:19 | Updated 2013-01-07 20:46:54 | Tags: non-human illumina yeast

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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?