<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div class="message-part" style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); padding-top: 10px; padding-right: 8px; padding-bottom: 10px; padding-left: 8px; border-top-width: 1px; border-top-style: solid; border-top-color: rgb(204, 204, 204); "><pre style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; font-family: monospace; white-space: pre-wrap !important; word-wrap: break-word; ">Hi. I ran the VEP web version using the first 750 SNPs in my large file. I had ticked on the following options:
1) Input file format : Ensembl default
2) Check for existing co-located variant : Yes and compare alleles
3) Show HGNC identifier for gene where available
4) SIFT predictions : Prediction and score
5) PolyPhen predictions : Prediction and score
6) Condel consensus (SIFT/PolyPhen) predictions : Prediction and score
This returned all the expected columns and values.
However, on downloading and running the stand-alone perl script using a config file which is as below:
terms ensembl
sift b
polyphen b
condel b
regulatory
gene
hgnc
ccds
check_ref
check_alleles
output_file myout
species homo_sapiens
format ensembl
input_file VEP_1.inp
The script does not return the HGNC or the rsID for co-located variants.
Any help on why this might be the case would be of great help.
Regards,
Aparna.
</pre></div><div class="message-htmlpart" style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); margin-top: 8px; margin-right: 8px; margin-bottom: 8px; margin-left: 8px; "><div class="rcmBody" style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); margin-top: 8px; margin-right: 8px; margin-bottom: 8px; margin-left: 8px; border-top-width: 0px; border-top-style: initial; border-top-color: initial; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span style="color: rgb(0, 0, 0); font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">Hi. I ran the VEP web version using the first 750 SNPs in my large file. I had ticked on the following options:</span><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); border-top-width: 0px; border-top-style: initial; border-top-color: initial; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">1) Input file format : Ensembl default</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">2) Check for existing co-located variant : Yes and compare alleles</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">3) Show HGNC identifier for gene where available</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">4) SIFT predictions : Prediction and score</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">5) PolyPhen predictions : Prediction and score</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">6) Condel consensus (SIFT/PolyPhen) predictions : Prediction and score</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">This returned all the expected columns and values.</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">However, on downloading and running the stand-alone perl script using a config file which is as below:</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); "><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); border-top-width: 0px; border-top-style: initial; border-top-color: initial; "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">terms ensembl</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">sift b</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">polyphen b</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">condel b</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">regulatory </div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">gene</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">hgnc</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">ccds</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">check_ref</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">check_alleles</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">output_file myout</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">species<span class="Apple-tab-span" style="white-space: pre; "> </span>homo_sapiens</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">format ensembl</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); ">input_file VEP_1.inp</div></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">The script does not return the HGNC or the rsID for co-located variants.</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">Any help on why this might be the case would be of great help.</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); "><br></div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">Regards,</div><div style="font-family: 'Lucida Grande', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">Aparna.</div><div><br></div></div></div></body></html>