Package org.snpsift
Class SnpSiftCmdDbNsfp
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdDbNsfp
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Annotate a VCF file with dbNSFP.
The dbNSFP is an integrated database of functional predictions from multiple algorithms for the comprehensive collection of human non-synonymous SNPs (NSs). Its current version (ver 1.1) is based on CCDS version 20090327 and includes a total of 75,931,005 NSs. It compiles prediction scores from four prediction algorithms (SIFT, Polyphen2, LRT and MutationTaster), two conservation scores (PhyloP and GERP++) and other related information.
References:
http://sites.google.com/site/jpopgen/dbNSFP
Paper: Liu X, Jian X, and Boerwinkle E. 2011. dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutation. 32:894-899.
- Author:
- lletourn
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
protected boolean
protected boolean
final String
protected int
protected int
protected int
protected DbNsfpEntry
protected DbNsfp
static final String
static final String
protected String
protected boolean
static final int
static final int
protected boolean
protected org.snpeff.fileIterator.VcfFileIterator
protected String
Fields inherited from class org.snpsift.SnpSift
args, BUILD, command, config, configFile, dataDir, dbFileName, dbTabix, dbType, debug, download, EMPTY_ARGS, errCount, genomeVersion, help, log, needsConfig, needsDb, needsGenome, numWorkers, output, quiet, REVISION, saveOutput, shiftArgs, SHOW_EVERY_VCFLINES, showVcfHeader, showVersion, SOFTWARE_NAME, suppressOutput, vcfHeaderAddProgramVersion, vcfHeaderProcessed, vcfInputFile, verbose, VERSION, VERSION_MAJOR, VERSION_NO_NAME, VERSION_SHORT
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
addHeaders
(org.snpeff.fileIterator.VcfFileIterator vcfFile) Add some lines to header before showing itboolean
Annotate a VCF entryboolean
annotate
(org.snpeff.vcf.VcfEntry vcfEntry) boolean
annotateFinish
(org.snpeff.fileIterator.VcfFileIterator vcfFile) boolean
annotateInit
(org.snpeff.fileIterator.VcfFileIterator vcfFile) Initialize annotation processvoid
Check that all fields to add are availablevoid
init()
Initialize default valuesvoid
Parse command line argumentsboolean
run()
List
<org.snpeff.vcf.VcfEntry> run
(boolean createList) Run annotation algorithmvoid
setFieldsNamesToAdd
(String fieldsNamesToAdd) void
setTabixCheck
(boolean tabixCheck) void
Show usage messageMethods inherited from class org.snpsift.SnpSift
cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb
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Field Details
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DBNSFP_VCF_INFO_PREFIX
- See Also:
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DEFAULT_FIELDS_NAMES_TO_ADD
- See Also:
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MIN_JUMP
public static final int MIN_JUMP- See Also:
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SHOW_EVERY
public static final int SHOW_EVERY- See Also:
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CONFIG_DBNSFP_DB_NAME
- See Also:
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fieldsToAdd
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fieldsDescription
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fieldsType
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annotateEmpty
protected boolean annotateEmpty -
annotateMissing
protected boolean annotateMissing -
collapseRepeatedValues
protected boolean collapseRepeatedValues -
inverseFieldSelection
protected boolean inverseFieldSelection -
tabixCheck
protected boolean tabixCheck -
vcfFileName
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count
protected int count -
countAnnotated
protected int countAnnotated -
countVariants
protected int countVariants -
dbNsfp
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vcfFile
protected org.snpeff.fileIterator.VcfFileIterator vcfFile -
currentDbEntry
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fieldsNamesToAdd
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Constructor Details
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SnpSiftCmdDbNsfp
public SnpSiftCmdDbNsfp() -
SnpSiftCmdDbNsfp
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Method Details
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addHeaders
public boolean addHeaders(org.snpeff.fileIterator.VcfFileIterator vcfFile) Add some lines to header before showing it- Specified by:
addHeaders
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
addHeaders
in classSnpSift
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annotate
Annotate a VCF entry- Parameters:
info
- Add values to 'info' map. Note that we may have some previous values in the map- Returns:
- True if entries were added to the map
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) -
annotateFinish
public boolean annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile) - Specified by:
annotateFinish
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateFinish
in classSnpSift
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annotateInit
public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile) Initialize annotation process- Specified by:
annotateInit
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateInit
in classSnpSift
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checkFieldsToAdd
Check that all fields to add are available- Throws:
IOException
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getFieldsType
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init
public void init()Initialize default values -
parseArgs
Parse command line arguments -
run
public boolean run() -
run
Run annotation algorithm -
setFieldsNamesToAdd
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setTabixCheck
public void setTabixCheck(boolean tabixCheck) -
usage
Show usage message
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