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Vcf cnv #800

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Merged
Peter-J-Freeman merged 3 commits into from
Apr 7, 2026
Merged

Vcf cnv #800

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5c9aa84
Merge pull request #798 from openvar/develop
Peter-J-Freeman Mar 27, 2026
9288ef1
Output VCF dels etc as in #799
Peter-J-Freeman Mar 27, 2026
7cc87a6
update table output lovd checking
Peter-J-Freeman Apr 7, 2026
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3 changes: 2 additions & 1 deletion VariantValidator/modules/valoutput.py
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Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,8 @@ def format_as_table(self, with_meta=True):
for variant in self.output_list:

# Get additional warnings from lovd syntax check
self.lovd_syntax_check(variant)
if variant.output_type_flag == 'warning':
self.lovd_syntax_check(variant)

prot = ''
if variant.hgvs_predicted_protein_consequence is not None:
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24 changes: 24 additions & 0 deletions VariantValidator/modules/vvMixinCore.py
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Expand Up @@ -1297,6 +1297,30 @@ def validate(self,
for build_key, accession_dict in list(lifted_response.items()):
try:
accession_key = list(accession_dict.keys())[0]
for k, v in accession_dict.items():
hgvs = v["hgvs_genomic_description"].posedit
edit = hgvs.edit

# Extract HGVS coordinates and edit type (do NOT mutate)
start = int(hgvs.pos.start.base)
end = int(hgvs.pos.end.base)
variant_type = edit.type # 'del', 'dup', 'inv'

# Only apply SV-style formatting for large variants
if (variant_type in ["del", "dup", "inv"]
and len(edit.ref) >= 50):

# Overwrite/standardise VCF-style fields if still needed
v["vcf"]["pos"] = str(start) # VCF left anchor convention
v["vcf"]["ref"] = str(end)
v["vcf"]["alt"] = variant_type.upper()

else:
# Small variants: keep original VCF-style representation
# (no SV transformation)
pass


if accession_dict[accession_key]['hgvs_genomic_description'].ac.startswith('NC_'):
primary_assembly_loci[build_key.lower()] = accession_dict[accession_key]
else:
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