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.
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