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mhguo1 / TRAPD

Burden testing against public controls
MIT License
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vep_annotation #8

Open asura117 opened 5 years ago

asura117 commented 5 years ago

Hi, I was just wondering how the _makesnpfile.py deals with annotations in different transcripts/genes of the same variation. Does the script only take into account only the first instance of the annotation (for example CADD score or CLINVAR) or does it parse through the entire record for all the canonical annotations to retain qualifying variants?

misrak commented 2 years ago

The input file for make_snpfile.py is a VCF file where in all the annotations (i.e. all the possible canonical transcripts are in one line) are clubbed together at one instance. Therefore, the script only takes the instance available to it to make the snpfile.txt.