Description

Scan a reference genome to get microsatellite & homopolymer information

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

FASTA file

*.{fa,fasta}

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 scan output file of homopolymers & minisatellites

*.msisensor_scan.txt
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