Description

Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

Output

Name
Description
Pattern

flagstat ()

versions ()

Tools

samtools Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT
nf-core pipelines with this module
blobtoolkitgenomeassemblyreadmappingvariantcalling
Authors