Description

msisensor2 detection of MSI regions.

Input

name:type
description
pattern

meta{:bash}

:map

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

tumor_bam{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

tumor_bam_index{:bash}

:file

BAM/CRAM/SAM index file

*.{bai,crai}

meta2{:bash}

:map

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

models{:bash}

:file

Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)

*/*

Output

name:type
description
pattern

msi{:bash}

meta{:bash}

:map

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

${prefix}{:bash}

:file

MSI classifications as a text file

distribution{:bash}

meta{:bash}

:map

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

${prefix}_dis{:bash}

:file

Read count distributions of MSI regions

somatic{:bash}

meta{:bash}

:map

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

${prefix}_somatic{:bash}

:file

Somatic MSI regions detected.

versions_msisensor2{:bash}

${task.process}{:bash}

:string

The name of the process

msisensor2{:bash}

:string

The name of the tool

msisensor2 2> >(grep Version) | sed 's/Version: v//g'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

msisensor2{:bash}

:string

The name of the tool

msisensor2 2> >(grep Version) | sed 's/Version: v//g'{:bash}

:eval

The expression to obtain the version of the tool

Tools

msisensor2

MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.

github.com/niu-lab/msisensor2 github.com/niu-lab/msisensor2/blob/master/README.md https://github.com/niu-lab/msisensor2
included in
sarek
maintainer
Github user adamrtalbot
get in touch
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