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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) 2024 Illumina, Inc.
                                                                     3.25.0
---------------------------------------------------------------------------

Utilities focused on supplementary annotation

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

COMMAND: AutoDownloadGenerate   auto download and generate Omim, Clinvar, Clingen, dbSNP
         EncryptNsa             Encrypts a given nsa file
         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
         clinvarPreview         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
         PhyloPPrimate          create PhyloP Primate database
         PrimateAi              create PrimateAI database
         PromoterAi             create PromoterAI 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
         CosmicDownloader       Cosmic downloader
         NsaTrimmer             trim Nsa file

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

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

SAUtils AutoDownloadGenerate

To make generating supplementary annotation files easier, we have provided an easier command that can be use instead of more granular subcommands. This subcommands basically integrate both download and generate subcommand. Currently, this subcommand support several data sources:

  • ClinVar

  • ClinGen

  • dbSNP

  • OMIM

  • COSMIC

You can download only, generate only, or both download and generate supplementary files. To use this subcommands, you have to prepare a json file that will be used as data sources information. Below is tutorial to use this subcommand to generate each data source.

AutoDownloadGenerate ClinVar

Below is the command to use AutoDownloadGenerate for ClinVar to download and generate supplementary files.

The json file for ClinVar should be formatted like below:

There is no need to modify the json entry for ClinVar and you can use as it is.

AutoDownloadGenerate ClinGen

The json file for ClinGen should be formatted like below:

There is no need to modify the json entry for ClinGen and you can use as it is.

AutoDownloadGenerate dbSNP

The json file for dbSNP should be formatted like below:

The json above is examplke for dbSNP version 156. If you want to use it for different version, adjust the version number and all entries in files to use the actual URL. If you only want to generate GRCh38, just remove the GRCh37 entries in the sourceFiles.

AutoDownloadGenerate OMIM

The json file for OMIM should be formatted like below:

There is no need to modify the json entry for OMIM and you can use as it is. You have to export OMIM API key as environment variable with name OmimApiKey.

AutoDownloadGenerate COSMIC

The json file for COSMIC should be formatted like below:

You have to adjust the version entry according to which COSMIC version you want. You also need to have COSMIC credentials and export it as environment variable with name Cosmic_ClientId, Cosmic_Username, and Cosmic_Password

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