VCF FOMAT information

[wang-wldlsw]

Hi Tobias,

First, GL，Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">
I guess the calculation method is log(P), but I'm not sure if that's correct. And how are the probabilities of each genotype calculated?

Second, RC Description="Raw high-quality read counts for the SV"
RCL Description="Raw high-quality read counts for the left control region"
RCR Description="Raw high-quality read counts for the right control region"
RCL RCR calculates the number of reads on the left and right sides of the structural variation (SV). But what is the region? Like 100bp on each side?
In addition, for example, the sequencing depth of a certain site is 150x. I found that the read value calculated by "samtools depth" at this location is 129, but the RCL and RCR value are more than 40000. Therefore, how did RCL and RCR calculate the read counts?

Thank you so much for your help.

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