Hello, I'm a beginner in bioinformatics. Recently, I called SNPs using illumina sequencing data using gatk HaplotypeCaller using diploid option. And then, I performed gatk GenotypeGVCFs to get a GVCF file. Here I have a question about GT field and PGT field.
ctg000220_np1212 1296462 . G *,A 2242.98 . AC=1,1;AF=0.500,0.500;AN=2;DP=79;ExcessHet=0.0000;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.81;QD=32.40;SOR=1.092 GT:AD:DP:GQ:PGT:PID:PL:PS 1|2:0,9,54:63:99:0|1:1296462_G_*:3015,2275,2240,405,0,216:1296462
I attached one representative SNP from my GVCF file. I interpreted that this SNP calling data indicated that 'G' is a reference allele and two alternate allele ( deletion and A). GT field is 1|2, indicating that among two chromosomes from parents one has deletion (G->) and the other has mutation (G->A). My question is why PGT field is 0|1? I cannot understand why 0 is in PGT field since there are two alternate alleles in this SNP position.
As I known, PGT field explain how the alternate alleles are phased in relation to one another (https://gatk.broadinstitute.org/hc/en-us/articles/360050354712-What-is-physical-phasing-). How 0|1 PGT value can explain the phase of two alternate alleles in this SNP?
Thank you for reading my question!
