Package org.snpsift

Class SnpSiftCmdDbNsfp

  • All Implemented Interfaces:
    org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
    public class SnpSiftCmdDbNsfp
extends SnpSift
    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

    • Field Detail

      • DBNSFP_VCF_INFO_PREFIX

        public static final java.lang.String DBNSFP_VCF_INFO_PREFIX
        See Also:
        Constant Field Values

      • DEFAULT_FIELDS_NAMES_TO_ADD

        public static final java.lang.String DEFAULT_FIELDS_NAMES_TO_ADD
        See Also:
        Constant Field Values

      • CONFIG_DBNSFP_DB_NAME

        public final java.lang.String CONFIG_DBNSFP_DB_NAME
        See Also:
        Constant Field Values

      • fieldsToAdd

        protected java.util.Map<java.lang.String,​java.lang.String> fieldsToAdd

      • fieldsDescription

        protected java.util.Map<java.lang.String,​java.lang.String> fieldsDescription

      • fieldsType

        protected java.util.Map<java.lang.String,​java.lang.String> fieldsType

      • annotateEmpty

        protected boolean annotateEmpty

      • annotateMissing

        protected boolean annotateMissing

      • collapseRepeatedValues

        protected boolean collapseRepeatedValues

      • inverseFieldSelection

        protected boolean inverseFieldSelection

      • tabixCheck

        protected boolean tabixCheck

      • vcfFileName

        protected java.lang.String vcfFileName

      • count

        protected int count

      • countAnnotated

        protected int countAnnotated

      • countVariants

        protected int countVariants

      • dbNsfp

        protected DbNsfp dbNsfp

      • vcfFile

        protected org.snpeff.fileIterator.VcfFileIterator vcfFile

      • fieldsNamesToAdd

        protected java.lang.String fieldsNamesToAdd

    • Constructor Detail

      • SnpSiftCmdDbNsfp

        public SnpSiftCmdDbNsfp()

      • SnpSiftCmdDbNsfp

        public SnpSiftCmdDbNsfp​(java.lang.String[] args)

    • Method Detail

      • addHeaders

        public boolean addHeaders​(org.snpeff.fileIterator.VcfFileIterator vcfFile)
        Add some lines to header before showing it
        Specified by:
        addHeaders in interface org.snpeff.snpEffect.VcfAnnotator
        Overrides:
        addHeaders in class SnpSift

      • annotate

        public boolean annotate​(org.snpeff.interval.Variant variant,
                        java.util.Map<java.lang.String,​java.lang.String> info)
        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

      • annotate

        public boolean annotate​(org.snpeff.vcf.VcfEntry vcfEntry)
        Specified by:
        annotate in interface org.snpeff.snpEffect.VcfAnnotator
        Overrides:
        annotate in class SnpSift

      • annotateFinish

        public boolean annotateFinish​(org.snpeff.fileIterator.VcfFileIterator vcfFile)
        Specified by:
        annotateFinish in interface org.snpeff.snpEffect.VcfAnnotator
        Overrides:
        annotateFinish in class SnpSift

      • annotateInit

        public boolean annotateInit​(org.snpeff.fileIterator.VcfFileIterator vcfFile)
        Initialize annotation process
        Specified by:
        annotateInit in interface org.snpeff.snpEffect.VcfAnnotator
        Overrides:
        annotateInit in class SnpSift

      • checkFieldsToAdd

        public void checkFieldsToAdd()
                      throws java.io.IOException
        Check that all fields to add are available
        Throws:
        java.io.IOException

      • getFieldsType

        public java.util.Map<java.lang.String,​java.lang.String> getFieldsType()

      • init

        public void init()
        Initialize default values
        Overrides:
        init in class SnpSift

      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Parse command line arguments
        Specified by:
        parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        parseArgs in class SnpSift

      • run

        public boolean run()
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift

      • run

        public java.util.List<org.snpeff.vcf.VcfEntry> run​(boolean createList)
        Run annotation algorithm

      • setFieldsNamesToAdd

        public void setFieldsNamesToAdd​(java.lang.String fieldsNamesToAdd)

      • setTabixCheck

        public void setTabixCheck​(boolean tabixCheck)

      • usage

        public void usage​(java.lang.String msg)
        Show usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift