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:map

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

input:file

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

*.{bam,cram,sam}

Output

name:type
description
pattern

bam

meta:map

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

*.{bam}

${prefix}.bam:map

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

*.{bam}

cram

meta:map

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

*.{bam}

${prefix}.cram:map

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

*.{cram}

sam

meta:map

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

*.{bam}

${prefix}.sam:map

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

*.{sam}

versions

versions.yml:file

File containing software versions

versions.yml

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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