<div dir="ltr">I believe if your output is is VCF format, all fields are output even if they are empty, because all fields are separated by pipes "|" and the order has to be retained.<div><br></div><div style>I believe what you had asked previously was for the dev team to give you an example of a annotated VCF with all fields filled in , and they pointed out correctly that this is not possible since the presence of certain fields will exclude other from being filled . As an example, a intergenic variant means that all the CDS, and protein info fields are necessarily empty.</div>
<div style><br></div><div style>However, if your output is the tab delimited version fields that contain no information and are stored in the Extra column should not be output if they are empty... </div><div style><br></div>
<div style>That is why I believe this to be a bug. </div><div style><br></div><div style>Cheers</div><div style>Duarte</div></div><div class="gmail_extra"><br clear="all"><div><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div>
</div>
<br><br><div class="gmail_quote">On Wed, May 22, 2013 at 11:32 AM, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066">
<div>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.<div><div class="h5"><br>
<br>
On 05/22/2013 12:01 PM, Duarte Molha wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<div>Hi Will</div>
<div><br>
</div>
<div>I came across another unexpected behavior that I
would like to report to you...</div>
<div>After running one of my VCF files a few variations
output an empty GMAF field like <br>
</div>
<div><br>
</div>
<div>GMAF=: <br>
</div>
<div><br>
</div>
<div>Here is one of the output lines in question : </div>
<div><br>
</div>
<div>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>here is the VCF line that produces it:</div>
<div><br>
</div>
<div>
<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>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><br>
</div>
<div>Best regards</div>
<div>
<br>
</div>
<div>Duarte</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
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<br>
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