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?
