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/Debug/netcoreapp3.1/SAUtils.dll
---------------------------------------------------------------------------
SAUtils                                             (c) 2021 Illumina, Inc.
Stromberg, Roy, Lajugie, Jiang, Li, and Kang                         3.18.0
---------------------------------------------------------------------------

Utilities focused on supplementary annotation

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

COMMAND: AaCon                create AA conservation database
         ancestralAllele      create Ancestral allele database from 1000Genomes data
         ClinGen              create 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
         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
         ExacScores           create ExAC gene scores 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
         GME Variome          create GME Variome database
         Gnomad               create gnomAD database
         Gnomad-lcr           create gnomAD low complexity region database
         GnomadGeneScores     create gnomAD gene scores 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

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

dotnet Nirvana/bin/Debug/netcoreapp3.1/SAUtils.dll clinvar
---------------------------------------------------------------------------
SAUtils                                             (c) 2021 Illumina, Inc.
Stromberg, Roy, Lajugie, Jiang, Li, and Kang                         3.18.0
---------------------------------------------------------------------------

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