[ensembl-dev] Empty GMAF field in VEP (possible bug?)

Wed May 22 11:32:13 BST 2013

Hello Duarte,

To my understanding it shouldn't be printed if it's empty like you said.

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.

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.

Regards,
Guillermo.

On 05/22/2013 12:01 PM, Duarte Molha wrote:
> Hi Will
>
> I came across another unexpected  behavior that I would like to report 
> to you...
> After running one of my VCF files a few variations output an empty 
> GMAF field like
>
> GMAF=:
>
> Here is one of the output lines in question :
>
> 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
>
>
> here is the VCF line that produces it:
>
> 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
>
> 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?
>
> Best regards
>
> Duarte
>
>
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