Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

normal_bam (file)

Coordinate sorted BAM/CRAM/SAM file from normal tissue

*.{bam,cram,sam}

normal_bai (file)

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

*.{bam,cram,sam}

tumor_bam (file)

Coordinate sorted BAM/CRAM/SAM file from tumor tissue

*.{bam,cram,sam}

tumor_bai (file)

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

*.{bam,cram,sam}

homopolymers (file)

Output file from MSIsensor scan module

*.msisensor_scan.tab

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

txt (file)

MSIsensor MSI final report file

*.output

txt (file)

MSIsensor MSI DIS report file

*.output_dis

txt (file)

MSIsensor MSI germline report file

*.output_germline

txt (file)

MSIsensor MSI somatic report file

*.output_somatic
author
Github user kevbrick
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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