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DP=0 and DP="." ~ GT with no reads

sletortsletort franceMember


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 :

GT:AD:DP:GQ:PGT:PID:PL  ./.:0,0:0:.:.:.:.

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 ?

thank you.



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