GT and GL fields in VCF file

GT and GL fields in VCF file

2

Hi!

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


VCF


SNP

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