<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000066">
<div class="moz-cite-prefix">Hello Duarte,<br>
<br>
To my understanding it shouldn't be printed if it's empty like you
said.<br>
<br>
I'm telling you this because when I started to use VEP I asked if
it was possible to print all the fields even if they empty. I was
told you cannot if you use VCF as output format.<br>
<br>
I wish they add an option you can force empty output to be printed
on VCF. Would make things a lot easier if you want to run other
scripts or parsers over VCF output.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
On 05/22/2013 12:01 PM, Duarte Molha wrote:<br>
</div>
<blockquote
cite="mid:CAGqkoEJMA+KKWcPSt-XELRVkw3ZCOcRH6n1QfYHCo7FdFLD2qQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div style="">Hi Will</div>
<div style=""><br>
</div>
<div style="">I came across another unexpected behavior that I
would like to report to you...</div>
<div style="">After running one of my VCF files a few variations
output an empty GMAF field like <br>
</div>
<div style=""><br>
</div>
<div style="">GMAF=: <br>
</div>
<div style=""><br>
</div>
<div style="">Here is one of the output lines in question : </div>
<div style=""><br>
</div>
<div style="">1_145075775_G/A 1:145075775 A
ENSG00000178104 ENST00000530740 Transcript
missense_variant 127 88 30 P/S Cct/Tct
rs76199660,COSM329521
alt_alleles=A;ENSP=ENSP00000435654;PolyPhen=possibly_damaging(0.739);Grantham=74;SIFT=deleterious(0);quality_score=113.16;AD=220,25;GT=0/1;CAROL=Deleterious(0.999);DP=247;GQ=99;CLIN_SIG=other;Condel=deleterious(0.715);GMAF=:;PL=153,0,6524;ZYG=HET;BLOSUM62=-1;EXON=1/46;IND=S100807505;HGNC=PDE4DIP;GERP++_RS=3.25</div>
<div><br>
</div>
<div><br>
</div>
<div style="">here is the VCF line that produces it:</div>
<div style=""><br>
</div>
<div style="">
<div>1 145075775 . G A 113.16 SNPhardFilter
AC=1;AF=0.056;AN=18;BaseQRankSum=-5.651;DP=1883;DS;Dels=0.00;FS=0.784;HRun=0;HaplotypeScore=26.7686;MQ=57.87;MQ0=0;MQRankSum=-0.030;QD=0.46;ReadPosRankSum=0.964;SB=-64.14;set=FilteredInAll
GT:AD:DP:GQ:PL 0/0:247,1:248:99:0,617,7876
0/0:249,0:250:99:0,644,8180 0/1:220,25:247:99:153,0,6524
0/0:95,0:95:99:0,247,3222
0/0:247,1:248:99:0,656,8350 0/0:249,1:250:99:0,598,8015
0/0:215,0:215:99:0,560,7164 0/0:164,0:164:99:0,415,5416
0/0:166,0:166:99:0,433,5729</div>
<div><br>
</div>
<div style="">I was expecting that if you do not have GMAF
information for any given variation the field simply would
not be output. Is this correct?</div>
<div style=""><br>
</div>
<div style="">Best regards</div>
<div style="">
<br>
</div>
<div style="">Duarte</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<br>
<div class="moz-signature"><br>
</div>
</body>
</html>