samtools

samtools flagstat

samtools flagstat

Version:
1.x
Identifier: TL_ec2a8d_a6.0b
Tool

Description


samtools flagstat in.sam|in.bam|in.cram Does a full pass through the input file to calculate and print statistics to stdout. Provides counts for each of 13 categories based primarily on bit flags in the FLAG field. Each category in the output is broken down into QC pass and QC fail, which is presented as "#PASS + #FAIL" followed by a description of the category.

Author(s)

  • Heng Li
  • Bob Handsaker
  • Jue Ruan
  • Colin Hercus
  • Petr Danecek

Code Repository

  • GitHub

    https://github.com/samtools/samtools

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