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Indel detection in pooled samples

jdavilajdavila Posts: 4Member

Hi to all,

Best Answer


  • jdavilajdavila Posts: 4Member

    I am using UnifiedGenotyper for calling variants in a pooled sample of 3 --using sample_ploidy 6-- and was having problems calling indels. After a little bit of tinkering, it seems the problem was caused by using the default value in --minIndelFrac which by default is set to 0.25, so I set it to 0.08 Would it be a good idea to automatically lower this default value in the case of higher ploidies?


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