Description

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.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

input{:bash}

:file

BAM/CRAM/SAM file, must be sorted by name, not coordinate

*.{bam,cram,sam}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{bam}

${prefix}.bam{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{bam}

cram{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{bam}

${prefix}.cram{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{cram}

sam{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{bam}

${prefix}.sam{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{sam}

versions_samtools{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:string

The command used to generate the version of the tool

Tools

samtools
MIT

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.

http://www.htslib.org http://www.htslib.org/doc/samtools https://github.com/samtools/samtools 10.1093/bioinformatics/btp352
maintainers
Github user sppearce
Github user GallVp
get in touch
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