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

]

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

]

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

]

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
included in
raredisease
maintainer
Github user peterpru
get in touch
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