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08-10-2013, 07:59 PM
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Member
Location: USA Join Date: Nov 2010
Posts: 56
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GATK ? How to out put all read numbers
Hi,
I have a question regarding GATK. I am trying to get SNP calls and the number of reads associated with it (AD). When i look at the data, the number reads is no greater than 99 either for reference or alternate SNPs. I came to know that GATK does subsampling. The question is what setting/ flag do i set to turn off the sampling and get all the reads associated with a site? Thanks in advance newbie |
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