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Cannot parse VEP Mastermind CSQ tags which contains URL #67

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nswh opened this issue Mar 9, 2021 · 1 comment
Open

Cannot parse VEP Mastermind CSQ tags which contains URL #67

nswh opened this issue Mar 9, 2021 · 1 comment

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@nswh
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nswh commented Mar 9, 2021

Whet the annotated VCF has Mastermind URL in CSQ tags, vcf2db.py throw the following error:

Traceback (most recent call last):
File "/opt/vcf2db/vcf2db.py", line 923, in
impacts_extras=a.impacts_field, aok=a.a_ok)
File "/opt/vcf2db/vcf2db.py", line 233, in init
self.load()
File "/opt/vcf2db/vcf2db.py", line 318, in load
i = self._load(self.cache, create=True, start=1)
File "/opt/vcf2db/vcf2db.py", line 311, in _load
self.insert(variants, expanded, keys, i, create=create)
File "/opt/vcf2db/vcf2db.py", line 340, in insert
v in variants)
File "/opt/vcf2db/vcf2db.py", line 809, in gene_info
impacts.extend(cls(e, impacts_headers[k]) for e in dk)
File "/opt/vcf2db/vcf2db.py", line 809, in
impacts.extend(cls(e, impacts_headers[k]) for e in dk)
File "/opt/conda/lib/python2.7/site-packages/geneimpacts/effect.py", line 530, in init
assert not "=" in effect_string
AssertionError

Script submitted is as below:

vcf2db.py
${VCF_IN}
${PED}
${DB_OUT}
--expand gt_types
--expand gt_ref_depths
--expand gt_alt_depths

Input files attached.
hg38validation_quartet.30t.vcf.gz

hg38validation_quartet.vcf.ped.txt

@brentp
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brentp commented Mar 9, 2021

Hi, unfortunately, these annotations are not supported. I'd accept a pull-request to fix this.

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