<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi everyone,<div><br></div><div>While unraveling the complex variants that can be encoded in the vcf format (<a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40">http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40</a>) I came to realize that I don't know how to submit some of these complex alleles to the ensembl variation API for effect prediction.</div><div>For simple SNP's and indels the situation is clearly described in the help pages. The problem I seem to be having is with complex alleles:</div><div><br></div><div>eg. when a SNP is directly followed by an deletion on a chromosome z</div><div>ref:<span class="Apple-tab-span" style="white-space:pre"> </span>ACGTAGA</div><div>var:<span class="Apple-tab-span" style="white-space:pre"> </span>ACA--GA</div><div><br></div><div>this can be encoded as 2 variants:</div><div>chr<span class="Apple-tab-span" style="white-space:pre"> </span>start<span class="Apple-tab-span" style="white-space:pre"> </span>stop<span class="Apple-tab-span" style="white-space:pre"> </span>variant<span class="Apple-tab-span" style="white-space:pre"> </span>strand</div><div>z<span class="Apple-tab-span" style="white-space:pre"> </span>3<span class="Apple-tab-span" style="white-space:pre"> </span>3<span class="Apple-tab-span" style="white-space:pre"> </span>G/A<span class="Apple-tab-span" style="white-space:pre"> </span>+</div><div>z<span class="Apple-tab-span" style="white-space:pre"> </span>4<span class="Apple-tab-span" style="white-space:pre"> </span>5<span class="Apple-tab-span" style="white-space:pre"> </span>TA/-<span class="Apple-tab-span" style="white-space:pre"> </span>+</div><div>but clearly none of these will have the functional consequence of the true allele namely:</div><div>z<span class="Apple-tab-span" style="white-space:pre"> </span>3<span class="Apple-tab-span" style="white-space:pre"> </span>5<span class="Apple-tab-span" style="white-space:pre"> </span>GTA/A<span class="Apple-tab-span" style="white-space:pre"> </span>+</div><div><span class="Apple-style-span" style="white-space: pre;">unfortunately</span> this kind of allele does not seem to return any response from the variation API</div><div><span class="Apple-tab-span" style="white-space:pre"><br></span></div><div>I can think of a simmilar situation for an insertion:</div><div><div>ref:<span class="Apple-tab-span" style="white-space: pre; "> </span>ACG-TAGA</div><div>var:<span class="Apple-tab-span" style="white-space: pre; "> </span>ACACTAGA</div></div><div><br></div><div>where:</div><div><div>chr<span class="Apple-tab-span" style="white-space: pre; "> </span>start<span class="Apple-tab-span" style="white-space: pre; "> </span>stop<span class="Apple-tab-span" style="white-space: pre; "> </span>variant<span class="Apple-tab-span" style="white-space: pre; "> </span>strand</div><div>z<span class="Apple-tab-span" style="white-space: pre; "> </span>3<span class="Apple-tab-span" style="white-space: pre; "> </span>3<span class="Apple-tab-span" style="white-space: pre; "> </span>G/A<span class="Apple-tab-span" style="white-space: pre; "> </span>+</div><div>z<span class="Apple-tab-span" style="white-space: pre; "> </span>4<span class="Apple-tab-span" style="white-space: pre; "> </span>3<span class="Apple-tab-span" style="white-space: pre; "> </span>-/C<span class="Apple-tab-span" style="white-space: pre; "> </span>+</div></div><div>will not have the same consequence as</div><div>z<span class="Apple-tab-span" style="white-space:pre"> </span>4<span class="Apple-tab-span" style="white-space:pre"> </span>3<span class="Apple-tab-span" style="white-space:pre"> </span>G/AC<span class="Apple-tab-span" style="white-space:pre"> </span>+</div><div><br></div><div><br></div><div>Or do I see this all wrong?</div><div>is there a way to submit alleles like these for effect prediction?</div><div><br></div><div><br></div><div>Kind regards,</div><div><br></div><div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; white-space: pre-wrap; "><br></span></div><div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; white-space: pre-wrap; ">Bram De Wilde, MD</span></div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; white-space: pre-wrap; ">Center for Medical Genetics Ghent (CMGG)
Ghent University Hospital
Medical Research Building (MRB), 2nd floor, room 120.050
De Pintelaan 185, B-9000 Ghent, Belgium
+32 9 332 4812 (phone) | +32 9 332 6549 (fax)
<a href="http://medgen.ugent.be/">http://medgen.ugent.be/</a>
<a href="mailto:Bram.DeWilde@UGent.be">Bram.DeWilde@UGent.be</a> </span></div><div><br></div></span><br class="Apple-interchange-newline">
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