VCF row validity

[warindrarto]

I'm currently working with a VCF file that contains this row (for example; header included):

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  -
chr1    761958  .       C       T       67      .       DP=39;VDB=0.0274;AF1=0.5;AC1=1;DP4=18,0,20,1;MQ=36;FQ=47;PV4=1,7.9e-17,1,1      PL      97,0,74

Now, I'm wondering, is it valid for the PL data column to stick out on its own? Shouldn't it be together in the previous column, semicolon-separated from other INFO values?

I'm only wondering because I've been trying to feed the VCF file to a filtering script, and the script seems to stumble on this oddity. If the row is indeed invalid, I'm going to try fix the initial pipeline that produced the VCF file. If not, then it's the script that needs fixing.

Thanks in advance .

[RockChalkJayhawk]

Seems like your file is not actually valid. You should have a GT entry in the format field, along with the sample name. If you don't have it, then you should remove the last column altogether.

[Knaus]

As RockChalkJayhawk said the GT flag in the Format column is missing, and the individual or sample as well. see http://www.1000genomes.org/wiki/Anal...mat-version-41 of what parameters the VCF format version 4.1 consists.

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