[ensembl-dev] Empty GMAF field in VEP (possible bug?)
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
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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