Description

Compute genome-wide STR profile

Input

Name (Type)
Description
Pattern

meta (map)

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

]

alignment_file (file)

BAM/CRAM file

*.{bam,cram}

alignment_index (file)

Index of the BAM/CRAM file

*.{bai,crai}

meta2 (map)

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

fasta (file)

The FASTA reference file

*.{fasta,fa}

meta3 (map)

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

fasta_fai (file)

The index of the FASTA reference 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

locus_tsv (file)

The locus TSV file

*.tsv

motif_tsv (file)

The motif TSV file

*.tsv

str_profile (file)

The JSON file containing the STR 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