Module key

Variant record samples key.

Constants

• ANCESTRAL_HAPLOTYPE_ID
  Unique identifier of ancestral haplotype (AHAP).
• CONDITIONAL_GENOTYPE_QUALITY
  Conditional genotype quality (GQ).
• COPY_NUMBER_CONFIDENCE_INTERVAL
  Confidence interval around copy number (CICN).
• EXPECTED_ALTERNATE_ALLELE_COUNTS
  Expected alternate allele counts (EC).
• FILTER
  Filter indicating if this genotype was “called” (FT).
• FORWARD_STRAND_READ_DEPTHS
  Read depth for each allele on the forward strand (ADF).
• GENOTYPE
  Genotype (GT).
• GENOTYPE_COPY_NUMBER
  Copy number genotype for imprecise events (CN).
• GENOTYPE_COPY_NUMBER_LIKELIHOODS
  Copy number genotype likelihood for imprecise events (CNL).
• GENOTYPE_COPY_NUMBER_POSTERIOR_PROBABILITIES
  Copy number posterior probabilities (CNP).
• GENOTYPE_COPY_NUMBER_QUALITY
  Copy number genotype quality for imprecise events (CNQ).
• GENOTYPE_LIKELIHOODS
  Genotype likelihoods (GL).
• GENOTYPE_POSTERIOR_PROBABILITIES
  Genotype posterior probabilities (GP).
• HAPLOTYPE_ID
  Unique haplotype identifier (HAP).
• HAPLOTYPE_QUALITY
  Haplotype quality (HQ).
• LENGTH
  Length of <*> reference block (LEN).
• LOCAL_ALTERNATIVE_ALLELE
  1-based indices into ALT, indicating which alleles are relevant (local) for the current sample (LAA).
• LOCAL_EXPECTED_ALTERNATE_ALLELE_COUNTS
  Local-allele representation of EC (LEC).
• LOCAL_FORWARD_STRAND_READ_DEPTHS
  Local-allele representation of ADF (LADF).
• LOCAL_GENOTYPE_LIKELIHOODS
  Local-allele representation of GL (LGL).
• LOCAL_GENOTYPE_POSTERIOR_PROBABILITIES
  Local-allele representation of GP (LGP).
• LOCAL_READ_DEPTHS
  Local-allele representation of AD (LAD).
• LOCAL_REVERSE_STRAND_READ_DEPTHS
  Local-allele representation of ADR (LADR).
• LOCAL_ROUNDED_GENOTYPE_LIKELIHOODS
  Local-allele representation of PL (LPL).
• LOCAL_ROUNDED_GENOTYPE_POSTERIOR_PROBABILITIES
  Local-allele representation of PP (LPP).
• MAPPING_QUALITY
  RMS mapping quality (MQ).
• NOVEL_VARIANT_QUALITY_SCORE
  Phred style probability score that the variant is novel (NQ).
• PHASE_SET
  Phase set (PS).
• PHASE_SET_LIST
  Phase set list (PSL).
• PHASE_SET_LIST_ORDINALS
  Phase set list ordinal (PSO).
• PHASE_SET_LIST_QUALITIES
  Phase set list quality (PSQ).
• PHASING_QUALITY
  Phasing quality (PQ).
• READ_DEPTH
  Read depth (DP).
• READ_DEPTHS
  Read depth for each allele (AD).
• RESERVED_LA
  Reserved (LA).
• REVERSE_STRAND_READ_DEPTHS
  Read depth for each allele on the reverse strand (ADR).
• ROUNDED_GENOTYPE_LIKELIHOODS
  Phred-scaled genotype likelihoods rounded to the closest integer (PL).
• ROUNDED_GENOTYPE_POSTERIOR_PROBABILITIES
  Phred-scaled genotype posterior probabilities rounded to the closest integer (PP).