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  • #1

    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
    Tags: None
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