Description

GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

aligment_files (file)

One or more sorted BAM/CRAM file(s)

*.{bam,cram}

alignment_indices (file)

The index/indices of the BAM/CRAM file(s)

*.{bai,crai}

ref_regions (file)

A reference set of regions to genotype in a BED-like format. The file should have following columns:

  1. The name of the chromosome on which the STR is located
  2. The start position of the STR on its chromosome
  3. The end position of the STR on its chromosome
  4. The motif length
  5. The repeat motif
*.bed

fasta (file)

The reference FASTA file

*.{fasta,fa}

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

vcf (file)

The resulting VCF file containing the genotypes

*.vcf

samplestats (file)

A tab-delimited file containing statistics for each sample

*.tab
author
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gangstr
GPL v3-or-later

GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

github.com/gymreklab/GangSTR 10.1093/nar/gkz501