Description

MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input

Input

name:type
description
pattern

meta:map

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

]

normal:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

normal_index:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

tumor:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

tumor_index:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

intervals:file

bed file containing interval information, optional

*.{bed}

fasta:file

Reference genome

*.{fasta}

msisensor_scan:file

Output from msisensor-pro/scan, containing list of msi regions

*.list

Output

name:type
description
pattern

output_report

meta:map

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

]

${prefix}:file

File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score

output_dis

meta:map

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

]

${prefix}_dis:file

File containing distribution results

output_germline

meta:map

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

]

${prefix}_germline:file

File containing germline results

output_somatic

meta:map

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

]

${prefix}_somatic:file

File containing somatic results

versions

versions.yml:file

File containing software versions

versions.yml

Tools

msisensorpro
Custom Licence

Microsatellite Instability (MSI) detection using high-throughput sequencing data.