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tertiary_map

William Rowell edited this page Nov 5, 2024 · 2 revisions

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

[^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.

PacBio WGS Variant Pipeline

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