issue #1022 - document why

SACGF · Aug 8, 2024 · c49beda · c49beda
1 parent d0c105d
commit c49beda
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/annotation/tasks/annotate_variants.py b/annotation/tasks/annotate_variants.py
@@ -200,6 +200,8 @@ def _unannotated_variants_to_vcf(genome_build: GenomeBuild, vcf_filename,
 
 
 def write_qs_to_vcf(vcf_filename, genome_build, qs, info_dict=VARIANT_GRID_INFO_DICT, use_accession=False):
+    # We had an issue with writing accessions in VEP, so use chrom names and the default VEP fasta instead
+    # @see https://github.com/Ensembl/ensembl-vep/issues/1635
     qs = qs.order_by("locus__contig__genomebuildcontig__order", "locus__position")
     if use_accession:
         chrom_key = "locus__contig__refseq_accession"