Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

mapped_bam (file)

mapped BAM/SAM file

*.{bam,sam}

meta2 (map)

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

]

unmapped_bam (file)

unmapped BAM file

*.bam

meta3 (map)

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

fasta (file)

fasta file containing genomic sequence information

*.{fasta,fa}

meta4 (map)

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

dict (file)

dict file containing a sequence dictionary for the fasta file

*.{dict}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

Zipped BAM file

*.bam

versions (file)

File containing software versions

versions.yml
maintainer
Github user lescai
get in touch
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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