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tertiary_map
William Rowell edited this page Nov 5, 2024
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2 revisions
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.