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 Nirvana 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 Nirvana/bin/Release/net6.0/SAUtils.dll
---------------------------------------------------------------------------
SAUtils                                             (c) 2023 Illumina, Inc.
Stromberg, Roy, Platzer, Siddiqui, Ouyang, et al                     3.21.0
---------------------------------------------------------------------------

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 Nirvana/bin/Release/net6.0/SAUtils.dll clinvar
---------------------------------------------------------------------------
SAUtils                                             (c) 2023 Illumina, Inc.
Stromberg, Roy, Platzer, Siddiqui, Ouyang, et al                     3.21.0
---------------------------------------------------------------------------

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 Extension	Description
.nsa	Small variant annotations (e.g. SNV, insertions, deletions, etc.)
.gsa	Compact variant annotations (e.g. SNV, insertions, deletions, etc.)
.idx	Index file
.nsi	Interval annotations (e.g. SV, CNVs, intervals)
.nga	Gene annotations
.npd	Conservation scores
.rma	Reference Minor allele
.gfs	Gene fusions source
.gfj	Gene fusions JSON
.schema	JSON schema