vcf snp genotype

[M&M]

I made snp calls on a set of 14 samples with samtools mpileup.

How do I determine the genotype call in a particular sample from the vcf file?

An example entry (some fields omitted for clarity) is:

chr10 4770821 G T,C,A 999 1/1:84,15,0,84,15,84,78,1,78,75:6:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:57,15,0,57,15,57,57,15,57,57:5:26 1/1:79,15,0,79,15,79,79,15,79,79:5:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:90,15,0,90,15,90,90,15,90,90:5:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:62,47,41,28,0,13,62,47,28,62:7:17 1/1:65,16,7,55,0,52,65,16,55,65:4:20 1/1:84,15,0,84,15,84,84,15,84,84:5:26

(GT: PL: DP: GQ)

I thought a GT field of 1/1 would mean the TT genotype, but all of the sample have this genotype, so I am confused as to where the other alternate snp calls are coming from? Also, what does it mean when all of the PL scores are 0?

Thanks!

[swbarnes2]

Here's the quote form the vcf format page, from the 1000 genomes project.

The all 0's probably means that you have no read there. Even your other ones have very low DP's. I'd check the pileup to see which columns mean which combination of alleles, and I wouldn't think much of the data at loci like that where the coverage is so poor.