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, conaining list of msi regions

*.list

Output

Name (Type)
Description
Pattern

meta (map)

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

]

output_report (file)

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

output_dis (file)

File containing distribution results

output_germline (file)

File containing germline results

output_somatic (file)

File containing somatic results

versions (file)

File containing software versions

versions.yml

list (file)

File containing microsatellite list

*.{list}
included in
sarek
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

msisensorpro
Custom Licence

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

github.com/xjtu-omics/msisensor-pro github.com/xjtu-omics/msisensor-pro/wiki https://github.com/xjtu-omics/msisensor-pro 10.1016/j.gpb.2020.02.001