Description

Merge STR profiles into a multi-sample STR profile

Input

Name (Type)
Description
Pattern

meta (map)

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

]

manifest (file)

A tab-delimited file containing the sample name, whether it’s case or control
and the paths to the corresponding STR profiles.
See here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files

*.{tsv,txt}

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

fasta (file)

The reference FASTA file

*.{fasta,fa}

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

fasta_fai (file)

The index of the reference FASTA file

*.fai

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

merged_profiles (file)

The merged STR profiles

*.multisample_profile.json
author
Github user nvnieuwk
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Tools

expansionhunterdenovo
Apache License 2.0

ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).

github.com/Illumina/ExpansionHunterDenovo github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md https://github.com/Illumina/ExpansionHunterDenovo