Description

filter/convert SAM/BAM/CRAM file

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

0 ()

1 ()

qname (file)

Optional file with read names to output only select alignments

*.{txt,list}

index_format (string)

Index format, used together with ext.args = '--write-index'

bai|csi|crai

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

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
asccblobtoolkitcurationpretextgenomeassemblygenomenotereadmappingtreevalvariantcalling
Authors