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
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). 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 Details

    • DBNSFP_VCF_INFO_PREFIX

      public static final String DBNSFP_VCF_INFO_PREFIX
      See Also:

    • DEFAULT_FIELDS_NAMES_TO_ADD

      public static final String DEFAULT_FIELDS_NAMES_TO_ADD
      See Also:

    • MIN_JUMP

      public static final int MIN_JUMP
      See Also:

    • SHOW_EVERY

      public static final int SHOW_EVERY
      See Also:

    • CONFIG_DBNSFP_DB_NAME

      public final String CONFIG_DBNSFP_DB_NAME
      See Also:

    • fieldsToAdd

      protected Map<String,String> fieldsToAdd

    • fieldsDescription

      protected Map<String,String> fieldsDescription

    • fieldsType

      protected Map<String,String> fieldsType

    • annotateEmpty

      protected boolean annotateEmpty

    • annotateMissing

      protected boolean annotateMissing

    • collapseRepeatedValues

      protected boolean collapseRepeatedValues

    • inverseFieldSelection

      protected boolean inverseFieldSelection

    • tabixCheck

      protected boolean tabixCheck

    • vcfFileName

      protected 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

    • currentDbEntry

      protected DbNsfpEntry currentDbEntry

    • fieldsNamesToAdd

      protected String fieldsNamesToAdd

  • Constructor Details

    • SnpSiftCmdDbNsfp

      public SnpSiftCmdDbNsfp()

    • SnpSiftCmdDbNsfp

      public SnpSiftCmdDbNsfp(String[] args)

  • Method Details

    • 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, Map<String,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 IOException
      Check that all fields to add are available
      Throws:
      IOException

    • getFieldsType

      public Map<String,String> getFieldsType()

    • init

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

    • parseArgs

      public void parseArgs(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 List<org.snpeff.vcf.VcfEntry> run(boolean createList)
      Run annotation algorithm

    • setFieldsNamesToAdd

      public void setFieldsNamesToAdd(String fieldsNamesToAdd)

    • setTabixCheck

      public void setTabixCheck(boolean tabixCheck)

    • usage

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