Description

FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM

Input

name:type
description
pattern

meta{:bash}

:map

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

unmapped_bam{:bash}

:file

unmapped BAM file

*.bam

meta2{:bash}

:map

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

mapped_bam{:bash}

:file

mapped BAM/SAM file

*.{bam,sam}

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘GRCh38’ ]

fasta{:bash}

:file

fasta file containing genomic sequence information

*.{fasta,fa}

meta4{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘GRCh38’ ]

dict{:bash}

:file

dict file containing a sequence dictionary for the fasta file

*.{dict}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

${prefix}.bam{:bash}

:file

Zipped BAM file

*.bam

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

fgbio
MIT

A set of tools for working with genomic and high throughput sequencing data, including UMIs

http://fulcrumgenomics.github.io/fgbio http://fulcrumgenomics.github.io/fgbio/tools/latest https://github.com/fulcrumgenomics/fgbio
included in
radseq
maintainer
Github user lescai
get in touch
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