GT and GL fields in VCF file

GT and GL fields in VCF file



This might sound completely stupid, lazy and silliest question. But please help in understanding these acronyms of VCF file. I did had a look at the format pdf of VCF file and I got further confused. So, I have my data in a VCF file version 4.2:


chr1 10043 . T C 21 PASS 3 GT:DP:FT:GQ:GL 1/0:8:PASS:20:-2.0739,-0.00379451,-27.336

chr1    10055    .    T    G    4    PASS    3    GT:DP:FT:GQ:GL    0/0:13:PASS:31:-0.00031839,-3.6121,-54.5012
chr1    10105    .    A    C    7    PASS    3    GT:DP:FT:GQ:GL    1/0:45:PASS:13:-1.58548,-0.0193946,-153.729

Now, what does GT here represent for, it stand for Genotype and the different values that I have for GT, what does that represents and consequence can they have on a SNP call? Can I also determine if the mutation is one copy or in both copies of gene ? If yes how?

For GQ, I guess it is a phred score with -10log10p and higher the better?


The genome used is hg19.


Please help.


Thank you




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