Should I use sorted.bam or clean_dedup_recalibrated.bam for getting the metrics using Picard?
Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). This time we used the new kit for exome sequencing. I am trying to collect the statistics like on-target and off-target alignment summary for my exome sequencing data. After some studies, I figured out the picard tool with this CollectHsMetrics option.
Do I need to use just sorted.bam file or cleaned, duplication marked and recalibrated bam file as input for picard-CollectHsMetrics tool?