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