Description

Parse all the supporting reads of putative somatic SVs using nanomonsv. After successful completion, you will find supporting reads stratified by deletions, insertions, and rearrangements. A precursor to “nanomonsv get”

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

Aligned BAM file

*.{bam}

bai{:bash}

:file

BAM index file

*.{bai}

Output

name:type
description
pattern

insertions{:bash}

meta{:bash}

:map

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

${prefix}.insertion.sorted.bed.gz{:bash}

:file

Gzipped BED file containing reads supporting insertions

*.{bed.gz}

insertions_index{:bash}

meta{:bash}

:map

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

${prefix}.insertion.sorted.bed.gz.tbi{:bash}

:file

Index for gzipped BED file containing reads supporting insertions

*.{bed.gz.tbi}

deletions{:bash}

meta{:bash}

:map

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

${prefix}.deletion.sorted.bed.gz{:bash}

:file

Gzipped BED file containing reads supporting deletions

*.{bed.gz}

deletions_index{:bash}

meta{:bash}

:map

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

${prefix}.deletion.sorted.bed.gz.tbi{:bash}

:file

Index for gzipped BED file containing reads supporting deletions

*.{bed.gz.tbi}

rearrangements{:bash}

meta{:bash}

:map

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

${prefix}.rearrangement.sorted.bedpe.gz{:bash}

:file

Gzipped BED file containing reads supporting rearrangements

*.{bed.gz}

rearrangements_index{:bash}

meta{:bash}

:map

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

${prefix}.rearrangement.sorted.bedpe.gz.tbi{:bash}

:file

Index for gzipped BED file containing reads supporting rearrangements

*.{bed.gz.tbi}

bp_info{:bash}

meta{:bash}

:map

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

${prefix}.bp_info.sorted.bed.gz{:bash}

:file

Gzipped BED file containing breakpoint info

*.{bed.gz}

bp_info_index{:bash}

meta{:bash}

:map

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

${prefix}.bp_info.sorted.bed.gz.tbi{:bash}

:file

Index for gzipped BED file containing breakpoint info

*.{bed.gz.tbi}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

nanomonsv
GPL v3

nanomonsv is a software for detecting somatic structural variations from paired (tumor and matched control) cancer genome sequence data.

github.com/friend1ws/nanomonsv github.com/friend1ws/nanomonsv#commands https://github.com/friend1ws/nanomonsv 10.1101/2020.07.22.214262
maintainer
Github user awgymer
get in touch
Ask a question on Slack Open an issue on GitHub