Samtools 1.7 rmdup + flagstat

This is a workflow that runs Samtools 1.7 rmdup  remove PCR duplicates and uses that output as input for Samtools 1.7 flagstat. Documentation for these apps can be found here:

Samtools 1.7 flagstat

Samtools 1.7 rmdup remove PCR duplicates

Tool Source for App

• Samtools 1.7 Manual