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:false ]

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

merged_profiles

meta:map

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

*.multisample_profile.json:file

The merged STR profiles

*.multisample_profile.json

versions

versions.yml:file

File containing software versions

versions.yml

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
Github user nvnieuwk
Ask a question on Slack Open an issue on GitHub