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

]

alignment_files:file

Alignment files

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

vcf

meta:map

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

]

*.vcf:file

The resulting VCF file containing the genotypes

*.vcf

samplestats

meta:map

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

]

*.samplestats.tab:file

A tab-delimited file containing statistics for each sample

*.tab

versions

versions.yml:file

File containing software versions

versions.yml

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
maintainer
Github user nvnieuwk
get in touch
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