diff --git a/src/main/resources/avro/bdg.avdl b/src/main/resources/avro/bdg.avdl index fbffe92..51e4537 100644 --- a/src/main/resources/avro/bdg.avdl +++ b/src/main/resources/avro/bdg.avdl @@ -795,6 +795,13 @@ record Genotype { */ union { boolean, null } phased = false; + /** + Phase set identifier, if any. Phased genotypes on the same contig with the same phaseSetId + are in the same phased set. All phased genotypes that do not have a phaseSetId are assumed to + belong to the same phased set. VCF genotype field reserved key PS. + */ + union { null, string } phaseSetId = null; + /** True if filters were applied for this variant. VCF genotype field reserved key FT any value other than the missing value. @@ -822,6 +829,37 @@ record GenotypeAnnotation { */ union { null, Genotype } genotype = null; + /** + Conditional genotype quality, encoded as a phred quality −10log10 p(genotype call is wrong + conditioned on the site being variant). VCF genotype field reserved key GQ. + */ + union { null, int } genotypeQuality = null; + + /** + Haplotype quality, encoded as two phred qualities. VCF genotype field reserved key HQ. + */ + array haplotypeQuality = []; + + /** + Phred-scaled probability that alleles are ordered incorrectly, against all other members in + the same phase set. VCF genotype field reserved key PQ. + */ + union { null, int } phaseSetQuality = null; + + /** + Root Mean Square (RMS) of the mapping quality of reads for this genotype. VCF genotype field + reserved key MQ. + */ + union { null, int } rmsMappingQuality = null; + + /** + Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias. + If set, the array should contain the number of reads that support the reference allele on the + forward strand, the reference allele on the reverse strand, the alternate allele on the forward + strand, and the alternate allele on the reverse strand, in that order. VCF genotype field key SB. + */ + array strandBias = []; + /** Additional genotype attributes that do not fit into the standard fields above. The values are stored as strings, even for flag, integer, and float types.