modules/
samtools_fixmate

Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.

fixmate samtools insert size repair bam paired read pairs

https://github.com/nf-core/modules/tree/master/modules/nf-core/samtools/fixmate

Description

Input

Name

Description

Pattern

`0` ()

`1` ()

Output

Name

Description

Pattern

`bam` ()

`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.

https://github.com/samtools/samtoolsdoi: 10.1093/bioinformatics/btp352License: MIT