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

[Duarte Molha]

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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