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Old 08-10-2013, 07:59 PM   #1
newbietonextgen
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Location: USA

Join Date: Nov 2010
Posts: 56
Wink 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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