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I've added population allele frequencies for 1000G to the tooltip.
. In other packages, I have tried running the model longer, but that hasn't seem to improve anything.…
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Need to save those allele frequencies and counts into the pickle and add a function to pull those instead.
Also need to decide which populations as the representative numbers vary wildly. https://m…
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#### Summary
I have a test case for a 4bp indel where the allele frequencies and reported probabilities look wrong, while changing the allele to be just an SNV gives the correct results.
#### Deta…
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Wondering if you are using site filters? As letting in too many bad indels will inflate the frameshift/lof frequencies
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We are interested in describing rates of migration among genetically similar populations. Given that they are genetically similar, we would expect to falsely identify some individuals as migrants. W…
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**User Story**
As a CAF Generator user, I want standardized fields in the outputted CAF so that I can reliably process the genotype and phenotype information when using CAFs for analysis.
Resourc…
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Hi,
Thank you for developing this great software.
I would like to calculate minor allele frequencies in each locus and did it using -doMaf 4 and beagle file.
I understand that PPmaf is minor all…
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For many downstream analysis it would be nice to also publish the VCF files with the ref/alternate allele and the frequencies.
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Hello.
Could you please clarify what exactly the flip.dosage=TRUE/FALSE does, when using the plinkCoxSurv function?
Apparently the flip.dosage is used to flip the allele, but it's not specified in t…