Description

msisensor2 detection of MSI regions.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

tumor_bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

normal_bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

intervals (file)

BED

*.bed

models (file)

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

*/*

Output

Name (Type)
Description
Pattern

meta (map)

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

]

msi (file)

MSI classifications as a text file

distribution (file)

Read count distributions of MSI regions

somatic (file)

Somatic MSI regions detected.

versions (file)

File containing software versions

versions.yml
maintainer
Github user adamrtalbot
get in touch
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Tools

msisensor2
GPL-3.0

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