Compute genome-wide STR profile
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
alignment_file
BAM/CRAM file
*.{bam,cram}
alignment_index
Index of the BAM/CRAM file
*.{bai,crai}
meta2
Groovy Map containing reference information e.g. [ id:‘test’ ]
fasta
The FASTA reference file
*.{fasta,fa}
meta3
fasta_fai
The index of the FASTA reference file
*.fai
versions
File containing software versions
versions.yml
locus_tsv
The locus TSV file
*.tsv
motif_tsv
The motif TSV file
str_profile
The JSON file containing the STR profile
*.json
ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).