Hello all, I am using GATK 184.108.40.206 for gCNV analysis of hundreds of exomes, and I can´t figure out if BAM input files must have the read duplicates marked or not for the default germline CNV analysis.
Thanks for the tutorial! Could you help me to understand her the NA19017.chr20sub.bam file was prepared? Is it just a BWA mapping reads? Does it got the sort and marked duplicates steps?