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i want to understand how to interpreat AD and calulate PL from it
I have a following INFO field from a haploid genome VCF file
What i understand is that
1) Genotype is 0 (reference).
2) 33,100 is the depth of reference and alternate
3) 133 is the total read depth (100+33)
4) 99 is the genotype quality
5) 0,141 is the PL.
My question is
I) if the supporting reads for alternate is more than the reference than can call be the reference genotype.
II) PL is basically used to confidently denote the genotype and according to this post low values mean a genotype is more likely, and high values means it’s less likely [https://gatkforums.broadinstitute.org/gatk/discussion/5913/math-notes-how-pl-is-calculated-in-haplotypecaller] . Thus probability of call being reference is high
If we get such contradictory results how to proceed.
Also based on the above info filed can we calculate the PL field? if yes can you please elaborate, I have checked few of your blogs but i could not find it [https://gatkforums.broadinstitute.org/gatk/discussion/5913/math-notes-how-pl-is-calculated-in-haplotypecaller].
In the above blog
# Conditional probabilities calculated by HC
P(AA | Data) = 0.000001
P(AT | Data) = 0.000100
P(TT | Data) = 0.010000
You havent clearly explained what is Data here?