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
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