tertiary_map.md

Tertiary Map File Specification

Type	Key	Description	Notes
File	slivar_js	slivar functions	link
File	ensembl_gff	Ensembl GFF3 reference annotation
File	lof_lookup	Path to table of loss-of-function scores per gene
File	clinvar_lookup	Path to table of ClinVar annotations per gene
File	slivar_gnotate_files	Comma-delimited array of population dataset allele frequencies in slivar gnotate format
String	slivar_gnotate_prefixes	Comma-delimieted array of prefixes to _af, _nhomalt, and _ac in slivar_gnotate_files
String (Float) 1	slivar_max_af	Maximum allele frequency within population for small variants
String (Int) 2	slivar_max_nhomalt	Maximum number of homozygous alternate alleles within population for small variants
String (Int) 2	slivar_max_ac	Maximum allele count within population for small variants
String (Int) 2	slivar_min_gq	Minimum genotype quality for small variants to be considered for compound heterozygous pairs
String	svpack_pop_vcfs	Comma-delimited array of structural variant population VCF paths
String	svpack_pop_vcf_indices	Comma-delimited array of structural variant population VCF index paths

Footnotes

1. Technically this value is interpreted as String by WDL, but slivar expects a Float, e.g, 0.03. ↩

2. Technically these values are interpreted as String by WDL, but slivar expects an Int. ↩ ↩² ↩³