| 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 | sawfish_exclude_bed | Regions to be excluded for Sawfish CNV calls in gzipped BED format | link |
| File | sawfish_exclude_bed_index | BED index | link |
| File | sawfish_expected_bed_male | Expected allosome copy number BED for XY samples | link |
| File | sawfish_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 |