Estimate repeat sizes using NGS data
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam
BAM/CRAM file
*.{bam,cram}
bai
Index of BAM/CRAM file
*.{bai,crai}
meta2
Groovy Map containing reference information e.g. [ id:‘test’ ]
fasta
Reference genome
*.{fna,fa,fasta}
meta3
fasta_fai
Reference genome index
*.fai
meta4
variant_catalog
JSON file with repeat expansion sites to genotype
*.json
Groovy Map containing sample information e.g. [ id:‘test’, gender:‘female’ ]
versions
File containing software versions
versions.yml
vcf
VCF with repeat expansions
*.vcf.gz
json
JSON with repeat expansions
*.json.gz
A tool for estimating repeat sizes
