hgmd deletions

Author: bpblanken

v03_pipeline/lib/reference_datasets/hgmd.py

@@ -12,6 +12,9 @@ def get_ht(path: str, reference_genome: ReferenceGenome) -> hl.Table:
         contig_recoding=reference_genome.contig_recoding(),
     )
     ht = mt.rows()
+    # HGMD represents DELETIONS as Structural Variants
+    # which is less than ideal.
+    ht = ht.filter(ht.alleles[1] != '<DEL>')
     return ht.select(
         **{
             'accession': ht.rsid,