Ju Jose
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Latest activity by Ju Jose-
Ju Jose created a post,
Do BAM file must have marked duplicates for germline CNV analysis?
AnsweredHello all, I am using GATK 4.2.5.0 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.
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Ju Jose commented,
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?