Description

Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data

Input

name:type
description
pattern

meta{:bash}

:map

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

normal_bam{:bash}

:file

Coordinate sorted BAM/CRAM/SAM file from normal tissue

*.{bam,cram,sam}

normal_bai{:bash}

:file

Index for coordinate sorted BAM/CRAM/SAM file from normal tissue

*.{bam,cram,sam}

tumor_bam{:bash}

:file

Coordinate sorted BAM/CRAM/SAM file from tumor tissue

*.{bam,cram,sam}

tumor_bai{:bash}

:file

Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue

*.{bam,cram,sam}

metascan{:bash}

:file

metascan file

homopolymers{:bash}

:file

Output file from MSIsensor scan module

*.msisensor_scan.tab

Output

name:type
description
pattern

output{:bash}

meta{:bash}

:map

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

${prefix}{:bash}

:file

Output file from MSIsensor msi module

output_dis{:bash}

meta{:bash}

:map

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

${prefix}_dis{:bash}

:file

Output file from MSIsensor module

output_germline{:bash}

meta{:bash}

:map

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

${prefix}_germline{:bash}

:file

Output file from MSIsensor module

output_somatic{:bash}

meta{:bash}

:map

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

${prefix}_somatic{:bash}

:file

Output file from MSIsensor module

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

msisensor
MIT

MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.

github.com/ding-lab/msisensor 10.1093/bioinformatics/btt755
maintainer
Github user kevbrick
get in touch
Ask a question on Slack Open an issue on GitHub