<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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?<div><br></div><div>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:<div><br><div><span class="Apple-tab-span" style="white-space: pre; "> </span>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.</div><div><br></div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>if chromStart == chromEnd: #SNV or indel with len(REF) == 2</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>POS = chromStart</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>elif chromStart == chromEnd-1: # indel with len(REF) == 1 and len(ALT) > 2 ( if len(REF) == len(ALT) == 2 POS would be chromStart)</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>POS = chromEnd</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>else:</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>POS = chromStart-1</div></div></div><div><br></div><div>
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