Field Detail

• TOTAL_SNPS

  public long TOTAL_SNPS

  The number of passing bi-allelic SNPs calls (i.e. non-reference genotypes) that were examined

• NUM_IN_DB_SNP

  public long NUM_IN_DB_SNP

  The number of passing bi-allelic SNPs found in dbSNP

• NOVEL_SNPS

  public long NOVEL_SNPS

  The number of passing bi-allelic SNPS called that were not found in dbSNP

• FILTERED_SNPS

  public long FILTERED_SNPS

  The number of SNPs that are filtered

• PCT_DBSNP

  public float PCT_DBSNP

  The fraction of passing bi-allelic SNPs in dbSNP

• DBSNP_TITV

  public double DBSNP_TITV

  The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites

• NOVEL_TITV

  public double NOVEL_TITV

  The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites

• TOTAL_INDELS

  public long TOTAL_INDELS

  The number of passing indel calls that were examined

• NOVEL_INDELS

  public long NOVEL_INDELS

  The number of passing indels called that were not found in dbSNP

• FILTERED_INDELS

  public long FILTERED_INDELS

  The number of indels that are filtered

• PCT_DBSNP_INDELS

  public float PCT_DBSNP_INDELS

  The fraction of passing indels in dbSNP

• NUM_IN_DB_SNP_INDELS

  public long NUM_IN_DB_SNP_INDELS

  The number of passing indels found in dbSNP

• DBSNP_INS_DEL_RATIO

  public double DBSNP_INS_DEL_RATIO

  The Insertion/Deletion ratio of the indel calls made at dbSNP sites

• NOVEL_INS_DEL_RATIO

  public double NOVEL_INS_DEL_RATIO

  The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites

• TOTAL_MULTIALLELIC_SNPS

  public double TOTAL_MULTIALLELIC_SNPS

  The number of passing multi-allelic SNP calls that were examined

• NUM_IN_DB_SNP_MULTIALLELIC

  public double NUM_IN_DB_SNP_MULTIALLELIC

  The number of passing multi-allelic SNPs found in dbSNP

• TOTAL_COMPLEX_INDELS

  public double TOTAL_COMPLEX_INDELS

  The number of passing complex indel calls that were examined

• NUM_IN_DB_SNP_COMPLEX_INDELS

  public double NUM_IN_DB_SNP_COMPLEX_INDELS

  The number of passing complex indels found in dbSNP

• SNP_REFERENCE_BIAS

  public double SNP_REFERENCE_BIAS

  The rate at which reference bases are observed at ref/alt heterozygous SNP sites.

• NUM_SINGLETONS

  public long NUM_SINGLETONS

  For summary metrics, the number of variants that appear in only one sample. For detail metrics, the number of variants that appear only in the current sample.

Constructor Detail

• VariantCallingSummaryMetrics

  public VariantCallingSummaryMetrics()

Method Detail

• getFileExtension

  public static String getFileExtension()

• calculateDerivedFields

  public void calculateDerivedFields()

  Description copied from class: MergeableMetricBase
  Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.

  Overrides:

  calculateDerivedFields in class MergeableMetricBase

• calculateFromDerivedFields

  public void calculateFromDerivedFields​(long totalHetDepth)

• foldInto

  public static <T extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics> void foldInto​(T target,
                                                                                                    Collection<T> metrics)