modules/smncopynumbercaller

tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.

copy numberBAMCRAMSMN1SMN2

https://github.com/nf-core/modules/[...]/modules/nf-core/smncopynumbercaller

Description

tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.

Input

name:type

description

pattern

`meta:map`

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

`bam:file`

BAM/CRAM file

*.{bam,cram}

`bai:file`

BAM/CRAM index file

*.{bai,crai}

Output

name:type

description

pattern

`smncopynumber`

`meta:map`

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

`out/*.tsv:file`

File containing the output of SMNCopyNumberCaller

*.{tsv}

`run_metrics`

`meta:map`

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

`out/*.json:file`

File containing run parameters of SMNCopyNumberCaller

*.{json}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

smncopynumbercaller
Apache License Version 2.0

call copy number of SMN1, SMN2, SMN2Δ7–8 from a bam file

github.com/Illumina/SMNCopyNumberCaller 10.1038/s41436-020-0754-0

modules/smncopynumbercaller

Description

Input

meta:map

bam:file

bai:file

Output

smncopynumber

meta:map

out/*.tsv:file

run_metrics

meta:map

out/*.json:file

versions

versions.yml:file

Tools

smncopynumbercaller Apache License Version 2.0

`meta:map`

`bam:file`

`bai:file`

`smncopynumber`

`meta:map`

`out/*.tsv:file`

`run_metrics`

`meta:map`

`out/*.json:file`

`versions`

`versions.yml:file`

smncopynumbercaller
Apache License Version 2.0