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Hi,
First of all, I want to commend you on creating an impressive tool—great work! I have a few comments and questions that I hope can help clarify some aspects:
1. MAF vs. EAF in GWAS Datasets…
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### What you did:
I looked at the GnomAD 4.1 data for variant chr2:79195912-G-T
https://gnomad.broadinstitute.org/variant/2-79195912-G-T?dataset=gnomad_r4
### What happened:
The foot of the …
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Hello,
Can you tell me, please, what is wrong with the attached files?
[example_geno.txt](https://github.com/user-attachments/files/16249970/example_geno.txt)
[punica_pop.txt](https://github.com/…
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From Noor Dawany
> I just wanted to bring to your attention that the CHOP cohort frequencies reported in Varify do not follow the conventional equation (from population genetics) for calculating alle…
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Hi,
I'm trying to run Admixture models on 93 samples from 12 populations with low coverage WGS data (~2.5X). I keep obtaining large log likelihoods with my models (see error output below), regardless…
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Hi @kcleal
What would be the best practice to estimate Structural Variant Allele Frequency for outputs generated from the Dysgu tool on a cohort of 300 samples? Currently, I'm trying to use `bcfto…
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Good afternoon:
I am new to bioinfirmatic, so please excuse i am asking something very obvious.
I am having a problem when calculateing the genome wide alleles frequencies. In the geno file apparent…
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Hello,
Thank you very much for a nice package!
My question is: can one use allelefrequencies data to calculate relative usage of different loci in a population or ethnic group? Does it actually …
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Linked to #152
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Hi
I have simulated some haploid data with Illumina error rates and ancient DNA data. It is ~25x coverage.
I wanted to see how the damage influences heterozygosity/genotype calls.
I noticed that …