ref_map

Reference Map File Specification

Type	Key	Description	Notes
String	name	Short name for reference	Alphanumeric characters, underscores, and dashes only. Will be used in file names.
File	fasta	Reference genome FASTA
File	fasta_index	Reference genome FASTA index
File	pbsv_splits	Regions for pbsv parallelization	below
File	pbsv_tandem_repeat_bed	Tandem Repeat BED used by PBSV to normalize SVs within TRs	link
File	trgt_tandem_repeat_bed	Tandem Repeat catalog (BED) for TRGT genotyping	link
File	hificnv_exclude_bed	Regions to be excluded by HIFICNV in gzipped BED format	link
File	hificnv_exclude_bed_index	BED index	link
File	hificnv_expected_bed_male	Expected allosome copy number BED for XY samples	link
File	hificnv_expected_bed_female	Expected allosome copy number BED for XX samples	link
File	pharmcat_positions_vcf	PharmCAT positions VCF
File	pharmcat_positions_vcf_index	PharmCAT positions VCF index

pbsv_splits

The pbsv_splits file is a JSON array of arrays of strings. Each inner array contains one or more chromosome names such that each inner array is of roughly equal size in base pairs. The inner arrays are processed in parallel. For example:

[
  ...
    [
        "chr10",
        "chr11"
    ],
    [
        "chr12",
        "chr13"
    ],
    [
        "chr14",
        "chr15"
    ],
  ...
]