understanding vcf format varscan output

[anneke bakelaar]

hello everybody,

I don't understand the meaning of the last column from varscan.
I make them red. maybe can somebody help me with it.

thanks




#fileformat=VCFv4.0
##source=VarScan2
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3 Sample4
chr1 177097 . C T PASS DP=12 GT: GQ: DP ./.:.:1 ./.:.:3 ./.:.:1 ./.:.:7
chr1 228494 . G A PASS DP=21 GT: GQ: DP ./.:.:2 0/0:1:8 ./.:.:1 1/1:2:10
chr1 318035 . C T PASS DP=212 GT: GQ: DP 0/1:4:66 0/0:5:66 0/0:1:14 0/0:5:66
chr1 324332 . A G PASS DP=71 GT: GQ: DP 0/1:2:21 ./.:.:19 0/0:1:9 0/0:0:22

[BasH]

This is described in the FORMAT field:

GT:GQ:DP

GT = Genotype (0/0 = homozygote reference, 1/1 homozygote alternate, 0/1 is heterozygous and -/- is no call.)
GQ = Genotype quality
DP = Read depth

see also: http://www.1000genomes.org/node/101