I have a couple of questions, I am working with GBS data and I am wondering if to lower the value of minReadsPerAlignmentStart (from 10 default to something lower) will help me to call more SNPs.
Just to be sure, the default mapping quality requiered for HC is 20 right? and the base quality 10?
I read a couple of issues about using the -ntc funtion for multi threads. If I am using GATK/3.5.0 there is a problem using -ntc?