Class FilterVcf

Field Details

• INPUT

  @Argument(shortName="I", doc="The INPUT VCF or BCF file.") public File INPUT

• OUTPUT

  @Argument(shortName="O", doc="The output VCF or BCF.") public File OUTPUT

• MIN_AB

  @Argument(doc="The minimum allele balance acceptable before filtering a site. Allele balance is calculated for heterozygotes as the number of bases supporting the least-represented allele over the total number of base observations. Different heterozygote genotypes at the same locus are measured independently. The locus is filtered if any allele balance is below the limit.") public double MIN_AB

• MIN_DP

  @Argument(doc="The minimum sequencing depth supporting a genotype before the genotype will be filtered out.") public int MIN_DP

• MIN_GQ

  @Argument(doc="The minimum genotype quality that must be achieved for a sample otherwise the genotype will be filtered out.") public int MIN_GQ

• MAX_FS

  @Argument(doc="The maximum phred scaled fisher strand value before a site will be filtered out.") public double MAX_FS

• MIN_QD

  @Argument(doc="The minimum QD value to accept or otherwise filter out the variant.") public double MIN_QD

• JAVASCRIPT_FILE

  @Argument(shortName="JS", doc="Filters a VCF file with a javascript expression interpreted by the java javascript engine. The script puts the following variables in the script context: \'variant\' a VariantContext ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/variantcontext/VariantContext.html ) and \'header\' a VCFHeader ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/vcf/VCFHeader.html ). Last value of the script should be a boolean to tell whether we should accept or reject the record.", optional=true) public File JAVASCRIPT_FILE