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:false ]

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}

metascan:file

metascan file

homopolymers:file

Output file from MSIsensor scan module

*.msisensor_scan.tab

Output

name:type
description
pattern

output

meta:map

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

${prefix}:file

Output file from MSIsensor msi module

output_dis

meta:map

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

${prefix}_dis:file

Output file from MSIsensor module

output_germline

meta:map

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

${prefix}_germline:file

Output file from MSIsensor module

output_somatic

meta:map

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

${prefix}_somatic:file

Output file from MSIsensor module

versions

versions.yml: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
Github user kevbrick
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