samtools_filteraligned

Filter out aligned reads from a BAM file.

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install samtools/filteraligned

https://github.com/CCBR/nf-modules/…/modules/CCBR/samtools/filteraligned/

Input

name	type	description
meta	map	Groovy Map containing reference information.
e.g. [ id:‘test’, single_end:false ]
bam	file	Input BAM file

Output

name	type	description	pattern
meta	map	Groovy Map containing reference information.
e.g. [ id:‘test’, single_end:false ]	NA
bam	file	Output BAM file with only reads that were not aligned	NA
versions	file	File containing software versions	versions.yml

Tools

samtools

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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.