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

[Will McLaren]

You are both correct, GMAF should not be printed if there is no data, I've
fixed this now.

Using VCF _does_ force empty output, since the pipe-separated consequence
string has a set number of fields defined in the header. If you ask for
--gmaf, then a field corresponding to GMAF will be added regardless of
whether there is data or not - it will just be empty in the absence of data
(i.e. appear as an empty string between two consecutive pipe characters).

You can also force empty fields by manually defining your fields using
--fields.

Regards,

Will


On 22 May 2013 11:32, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  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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