Skip to main content
Version: 3.22

SAUtils

Overview

SAUtils is a utility tool that creates binary supplementary annotation files (.nsa, .gsa, .npd, .nsi, etc.) from original data files (e.g. VCFs, TSVs, XML, HTML, etc.) for various data sources (e.g. ClinVar, dbSNP, gnomAD, etc.). These binary files can be fed into the Illumina Connected Annotations Annotation engine to provide supplementary annotations in the output.

The SAUtils Menu

SAUtils supports building binary files for many data sources. The help menu lists them out in the form of sub-commands.

dotnet SAUtils.dll
---------------------------------------------------------------------------
SAUtils (c) 2023 Illumina, Inc.
3.22.0
---------------------------------------------------------------------------

Utilities focused on supplementary annotation

USAGE: dotnet SAUtils.dll <command> [options]

COMMAND: AutoDownloadGenerate auto download and generate Omim, Clinvar, Clingen
AaCon create AA conservation database
ancestralAllele create Ancestral allele database from 1000Genomes data
ClinGen create ClinGen database
Downloader download ClinGen database
clinvar create ClinVar database
concat merge multiple NSA files for the same data source having non-overlapping regions
Cosmic create COSMIC database
CosmicSv create COSMIC SV database
CosmicFusion create COSMIC gene fusion database
CosmicCGC create COSMIC cancer gene census database
CustomGene create custom gene annotation database
CustomVar create custom variant annotation database
Dann create DANN database
Dbsnp create dbSNP database
Dgv create DGV database
DiseaseValidity create disease validity database
DosageMapRegions create dosage map regions
DosageSensitivity create dosage sensitivity database
DownloadOmim download OMIM database
ExtractMiniSA extracts mini SA
ExtractMiniXml extracts mini XML (ClinVar)
FilterSpliceNetTsv filter SpliceNet predictions
FusionCatcher create FusionCatcher database
Gerp create GERP conservation database
GlobalMinor create global minor allele database
Gnomad create gnomAD database
Gnomad-lcr create gnomAD low complexity region database
GnomadGeneScores create gnomAD gene scores database
GnomadSV create gnomAD structural variant database
Index edit an index file
MitoHet create mitochondrial Heteroplasmy database
MitomapSvDb create MITOMAP structural variants database
MitomapVarDb create MITOMAP small variants database
Omim create OMIM database
OneKGen create 1000 Genome small variants database
OneKGenSv create 1000 Genomes structural variants database
OneKGenSvVcfToBed convert 1000 Genomes structural variants VCF file into a BED-like file
PhyloP create PhyloP database
PrimateAi create PrimateAI database
RefMinor create Reference Minor database from 1000 Genome
RemapWithDbsnp remap a VCF file given source and destination rsID mappings
Revel create REVEL database
SpliceAi create SpliceAI database
TopMed create TOPMed database
Gme create GME Variome database
Decipher create Decipher database

You can get further detailed help for each sub-command by typing in the subcommand. For example:

dotnet SAUtils.dll clinvar
---------------------------------------------------------------------------
SAUtils (c) 2023 Illumina, Inc.
3.22.0
---------------------------------------------------------------------------

USAGE: dotnet SAUtils.dll clinvar [options]
Creates a supplementary database with ClinVar annotations

OPTIONS:
--ref, -r <VALUE> compressed reference sequence file
--rcv, -i <VALUE> ClinVar Full release XML file
--vcv, -c <VALUE> ClinVar Variation release XML file
--out, -o <VALUE> output directory
--help, -h displays the help menu
--version, -v displays the version

More detailed instructions about each sub-command can be found in documentation of respective data sources.

Output File Formats

The format of the binary file SAUtils produce depend on the type of annotation data represented in that file (e.g. small variant vs. structural variants vs. genes).

File ExtensionDescription
.nsaSmall variant annotations (e.g. SNV, insertions, deletions, etc.)
.gsaCompact variant annotations (e.g. SNV, insertions, deletions, etc.)
.idxIndex file
.nsiInterval annotations (e.g. SV, CNVs, intervals)
.ngaGene annotations
.npdConservation scores
.rmaReference Minor allele
.gfsGene fusions source
.gfjGene fusions JSON
.schemaJSON schema