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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
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vcf_extractor fails to find VEP format for CSQ score model? #67

Closed dnil closed 7 years ago

dnil commented 7 years ago

Hi,

I'm trying genmod on some VEP-annotated files with a CSQ-score model. I think I've got the csq_key names down just fine, but just when the config check is done ok, I get an error from vcf_extractor anyway. There is a format line in the vcf header, but perhaps the format is not quite the expected? Tested with a local vep83 and the example small vep vcf. Unfortunately no official test ini with csq - perhaps that's an idea for the future?

File "/home/daniel/anaconda3/envs/genmod/lib/python2.7/site-packages/extract_vcf/plugin.py", line 127, in get_entry raise IOError("If CSQ the csq format must be provided") IOError: If CSQ the csq format must be provided

moonso commented 7 years ago

👍 i will look into this. Could you send the score model?

moonso commented 7 years ago

How does your CSQ description look like in the VCF header?