Module noodles_vcf::record::info::field::key

VCF record info key.

Structs

• Other
  A non-reserved VCF header info key.

Enums

• Key
  A VCF header info key.
• ParseError
  An error returned when a raw VCF record info field key fails to parse.
• Standard
  A VCF header info key.

Constants

• ADJACENT_COPY_NUMBER
  Copy number of adjacency (CNADJ).
• ADJACENT_COPY_NUMBER_CONFIDENCE_INTERVALS
  Confidence interval around copy number for the adjacency (CICNADJ).
• ADJACENT_READ_DEPTHS
  Read Depth of adjacency (DPADJ).
• ALLELE_COUNT
  Allele count in genotypes, for each ALT allele, in the same order as listed (AC).
• ALLELE_FREQUENCIES
  Allele frequency for each ALT allele in the same order as listed (AF).
• ANCESTRAL_ALLELE
  Ancestral allele (AA).
• BASE_QUALITY
  RMS base quality (BQ).
• BREAKEND_CONFIDENCE_INTERVALS
  Confidence interval around the inserted material between breakends (CILEN).
• BREAKEND_COPY_NUMBER
  Copy number of segment containing breakend (CN).
• BREAKEND_EVENT_ID
  ID of event associated to breakend (EVENT).
• BREAKPOINT_IDS
  ID of the assembled alternate allele in the assembly file (BKPTID).
• CIGAR
  Cigar string describing how to align an alternate allele to the reference allele (CIGAR).
• COPY_NUMBER_CONFIDENCE_INTERVALS
  Confidence interval around copy number for the segment (CICN).
• DBV_ID
  ID of this element in Database of Genomic Variation (DBVID).
• DB_RIP_ID
  ID of this element in DBRIP (DBRIPID).
• DB_VAR_ID
  ID of this element in DBVAR (DBVARID).
• END_CONFIDENCE_INTERVALS
  Confidence interval around END for imprecise variants (CIEND).
• END_POSITION
  End position of the variant described in this record (END).
• EVENT_TYPE
  Type of associated event (EVENTTYPE).
• FORWARD_STRAND_READ_DEPTHS
  Read depth for each allele on the forward strand (ADF).
• IS_IMPRECISE
  Imprecise structural variation (IMPRECISE).
• IS_IN_1000_GENOMES
  1000 Genomes membership (1000G).
• IS_IN_DB_SNP
  dbSNP membership (DB).
• IS_IN_HAP_MAP_2
  HapMap2 membership (H2).
• IS_IN_HAP_MAP_3
  HapMap3 membership (H3).
• IS_NOVEL
  Indicates a novel structural variation (NOVEL).
• IS_SOMATIC_MUTATION
  Somatic mutation (SOMATIC).
• IS_VALIDATED
  Validated by follow-up experiment (VALIDATED).
• MAPPING_QUALITY
  RMS mapping quality (MQ).
• MATE_BREAKEND_IDS
  ID of mate breakends (MATEID).
• MICROHOMOLOGY_LENGTHS
  Length of base pair identical micro-homology at event breakpoints (HOMLEN).
• MICROHOMOLOGY_SEQUENCES
  Sequence of base pair identical micro-homology at event breakpoints (HOMSEQ).
• MOBILE_ELEMENT_INFO
  Mobile element info of the form NAME,START,END,POLARITY (MEINFO).
• MOBILE_ELEMENT_TRANSDUCTION_INFO
  Mobile element transduction info of the form CHR,START,END,POLARITY (METRANS).
• PARTNER_BREAKEND_ID
  ID of partner breakend (PARID).
• POSITION_CONFIDENCE_INTERVALS
  Confidence interval around POS for imprecise variants (CIPOS).
• REPEAT_UNIT_BASE_COUNTS
  Number of bases in each individual repeat unit (RUB).
• REPEAT_UNIT_COUNTS
  Repeat unit count of corresponding repeat sequence (RUC).
• REPEAT_UNIT_COUNT_CONFIDENCE_INTERVALS
  Confidence interval around RUC (CIRUC).
• REPEAT_UNIT_LENGTHS
  Repeat unit length of the corresponding repeat sequence (RUL).
• REPEAT_UNIT_SEQUENCES
  Repeat unit sequence of the corresponding repeat sequence (RUS).
• REVERSE_STRAND_READ_DEPTHS
  Read depth for each allele on the reverse strand (ADR).
• SAMPLES_WITH_DATA_COUNT
  Number of samples with data (NS).
• STRAND_BIAS
  Strand bias (SB).
• SV_CLAIM
  Copy number of adjacency (CNADJ).
• SV_LENGTHS
  Difference in length between REF and ALT alleles (SVLEN).
• SV_TYPE
  Type of structural variant (SVTYPE).
• TOTAL_ALLELE_COUNT
  Total number of alleles in called genotypes (AN).
• TOTAL_DEPTH
  Combined depth across samples (DP).
• TOTAL_READ_DEPTHS
  Total read depth for each allele (AD).
• TOTAL_REPEAT_SEQUENCE_BASE_COUNTS
  Total number of bases in the corresponding repeat sequence (RB).
• TOTAL_REPEAT_SEQUENCE_BASE_COUNT_CONFIDENCE_INTERVALS
  Confidence interval around RB (CIRB).
• TOTAL_REPEAT_SEQUENCE_COUNTS
  Total number of repeat sequences in this allele (RN).
• ZERO_MAPPING_QUALITY_COUNT
  Number of MAPQ == 0 reads (MQ0).