Entering edit mode
6.2 years ago
Leon
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130
CollectHsMetrics
Hi, I wanna calculate enrichment efficiency using Picard CollectHsMetrics, however I do not know which items correspond to enrichment efficiency. The command is gatk CollectHsMetrics -I dedup.bam -O hs_metrics.txt -BI list.interval_list -TI list.interval_list -R hs38DH.fa I am further confused after reviewed Picard metrics definitions document(https://broadinstitute.github.io/picard/javadoc/picard/picard/analysis/directed/HsMetrics.html). Any one has experience with this tool?
enrichment efficiency = Number PF(passing filter) reads mapping to targets/Total number of PF reads mapping to the reference