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:map

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

bam:file

Aligned BAM file

*.{bam}

bai:file

BAM index file

*.{bai}

Output

name:type
description
pattern

insertions

meta:map

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

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

Gzipped BED file containing reads supporting insertions

*.{bed.gz}

insertions_index

meta:map

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

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

Index for gzipped BED file containing reads supporting insertions

*.{bed.gz.tbi}

deletions

meta:map

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

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

Gzipped BED file containing reads supporting deletions

*.{bed.gz}

deletions_index

meta:map

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

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

Index for gzipped BED file containing reads supporting deletions

*.{bed.gz.tbi}

rearrangements

meta:map

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

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

Gzipped BED file containing reads supporting rearrangements

*.{bed.gz}

rearrangements_index

meta:map

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

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

Index for gzipped BED file containing reads supporting rearrangements

*.{bed.gz.tbi}

bp_info

meta:map

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

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

Gzipped BED file containing breakpoint info

*.{bed.gz}

bp_info_index

meta:map

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

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

Index for gzipped BED file containing breakpoint info

*.{bed.gz.tbi}

versions

versions.yml: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
Github user awgymer
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