[ensembl-dev] how to get original VCF file's POS from variant effect predictor output?

[Michael Yourshaw]

In order to associate the output of the variant effect predictor back to the original VCF 4.0 file, I need to be able to determine the value of the POS field of the VCF file from data in the VEP output. How can I do this?

At the risk of revealing my ignorance of VCF format and algebra, I think the following works, but it depends on there never being a VCF where len(REF) == len(ALT) == 2 — I am not sure this is a safe assumption:

	get chromStart and chromEnd from the VEP Location field (chromEnd=chromStart if not chromEnd). Can’t use Uploaded variation, which might get turned into rs ID.

	if chromStart == chromEnd: #SNV or indel with len(REF) == 2
		POS = chromStart
	elif chromStart == chromEnd-1: # indel with len(REF) == 1 and len(ALT) > 2 ( if len(REF) == len(ALT) == 2 POS would be chromStart)
		POS = chromEnd
	else:
		POS = chromStart-1


ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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