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

]

bam (file)

Aligned BAM file

*.{bam}

bai (file)

BAM index file

*.{bai}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

insertions (file)

Gzipped BED file containing reads supporting insertions

*.{bed.gz}

insertions_index (file)

Index for gzipped BED file containing reads supporting insertions

*.{bed.gz.tbi}

deletions (file)

Gzipped BED file containing reads supporting deletions

*.{bed.gz}

deletions_index (file)

Index for gzipped BED file containing reads supporting deletions

*.{bed.gz.tbi}

rearrangements (file)

Gzipped BED file containing reads supporting rearrangements

*.{bed.gz}

rearrangements_index (file)

Index for gzipped BED file containing reads supporting rearrangements

*.{bed.gz.tbi}

bp_info (file)

Gzipped BED file containing breakpoint info

*.{bed.gz}

bp_info_index (file)

Index for gzipped BED file containing breakpoint info

*.{bed.gz.tbi}

versions (file)

File containing software versions

versions.yml
author
Github user awgymer
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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