Additional genotype annotation fields

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<int> 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<int> 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.