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DP=0 and DP="." ~ GT with no reads
Sometimes when a sample has no reads, it still can have a genotype.
I used GenotypeGVCFs (without CombineGVCFs) to generate a vcf with several samples.
If I extract data for one sample, I sometimes see missing genotype with no read :
which seem ok to me. Note that DP = 0.
but more rarely, I see a genotype with no read :
GT:AD:DP:GQ:PGT:PID:PL 0/0:0,0:.:3:.:.:0,3,45 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,0:.:3:1|1:32486973_A_AG:45,3,0
and this is more questionnable. Note that DP = "."
Can you explain how genotype can be called without reads ? (I suspect haplotype to be involved, but without read I do not understand)
any idea about the DP value ? why has it a value with missing genotype ?