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16 months ago
pragnapcu
▴
10
I am wondering how the number of reads are more in haplotypecaller bam than in baserecalibrator bam though they dont appear to be duplicates?
show us the data please.
As per explanation given here https://gatk.broadinstitute.org/hc/en-us/articles/360040096812-HaplotypeCaller#--bam-output , I noticed two categories of reads in the bam generated from GATK HaplotypeCaller. One set of reads start with HC and another set has original read name.
Can Someone help me in better understanding this scenario.