DiagnoseTarget output questions
Is DiagnoseTargets counting only reads that have mapped uniquely? Is that one of the default filters?
From the vcf I see that
IDP - Average depth across the interval. Sum of the depth in a loci divided by interval size.
LL - Number of loci for this sample, in this interval with low coverage (below the minimum coverage) but not zero
ZL - Number of loci for this sample, in this interval with zero coverage.
I'm interested in the total number of reads mapped to each interval.
Is this true that IDP = #reads_in_this_interval/(LL+ZL) ?
so if I want to extract #reads_in_this_interval, I can look at IDP*(LL+ZL)? I have different number of reads in each sample, so I first need to normalize it.