<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; ">
<div>
<div style="color: rgb(0, 0, 0); ">Hi developers of VEP,</div>
<div style="color: rgb(0, 0, 0); "><br>
</div>
<div style="color: rgb(0, 0, 0); ">It was great using the latest version of your tool (v2.3) 'Variant effect Predictor' which looks promising. We were actually interested in the standalone version of your software but encountered some issues when trying to
use the script with the —cache option on mac. There was some issue with the reading of the transcript data in the cache, though gzip and zcat utilities were installed on the local machine (basically a mac environment and not linux). The errors that I get
are:</div>
<div style="color: rgb(0, 0, 0); "><br>
</div>
<div><font class="Apple-style-span" color="#2c2cfb">~/.vep/homo_sapiens/65/1/1-1000000.gz.Z: No such file or directory</font> </div>
<div><br>
</div>
<div><font class="Apple-style-span" color="#2c2cfb">Magic number checking on storable file failed</font></div>
<div><font class="Apple-style-span" color="#2c2cfb"><br>
</font></div>
<div><b>We were wondering if that could be fixed by some means. It would be a great help!</b></div>
<div style="color: rgb(0, 0, 0); "><br>
</div>
<div style="color: rgb(0, 0, 0); ">Secondly, if we understand correctly, the –sift and –polyphen options were lately introduced and are not in terms with the –vcf option. It would have been great if we could see the polyphen and sift predictions under 'CSQ'
of an output vcf file, when we choose the three output options as;</div>
<div style="color: rgb(0, 0, 0); ">--sift —polyphen —vcf</div>
<div style="color: rgb(0, 0, 0); ">We understand it has been clearly documented that the –vcf option only displays consequence type, but it would be of great use if the —vcf option was available in conjugation with the —sift and —polyphen options. <b>Please
let us know if you could make that option available to us.</b></div>
<div style="color: rgb(0, 0, 0); "><br>
</div>
<div style="color: rgb(0, 0, 0); ">Regards,</div>
<div style="color: rgb(0, 0, 0); "><br>
</div>
<div style="color: rgb(0, 0, 0); ">Uma D.Paila (Ph.D),</div>
<div style="color: rgb(0, 0, 0); ">Research Associate with Dr. Aaron Quinlan,</div>
<div style="color: rgb(0, 0, 0); ">Center for Public Health Genomics,</div>
<div style="color: rgb(0, 0, 0); ">University of Virginia, VA</div>
</div>
</body>
</html>