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This isn't supported in Zarr yet but because it is in Dask and the majority of genotyping data sets have major alleles with high frequency, there may be some significant speedups resulting from a spar…
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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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## [Viral data.ipynb](https://github.com/maousi/HBV/blob/master/Viral%20data.ipynb)
You are looking at [NA values](http://localhost:8888/notebooks/Viral%20data.ipynb#NA-values). Plot 54 is great. I…
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I'm getting this error when trying to run vt genotype
```
[parlar@mps 12191-96]$ vt genotype -r /home/bcbio_root/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -s 12191-96 -b 12191-96-ready.bam -o 121…
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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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VAT will query vat-dp mainly with variant ID for now.
Other than genotypes, what information will be provided by vat-dp? Allele frequency, DP, Allele Count, etc? or these information will be provide…
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The following are the items raised so far.
- [ ] select a variant by rsid or index within the region selected
- [ ] getindex function
- [ ] major/minor alleles for haplotypes
- [x] ref allele d…
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It would be nice to have the ability to filter variants based on the alternate allele frequency in specific subsets of individuals. Currently, we can filter based on the counts of specific genotypes, …
arq5x updated
8 years ago
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Hi,
What is the general performance expectation for highly polygenic GWAS, with hundreds of GWAS-sig loci?
I am running GCTA-COJO conditional analysis on a case:control GWAS with hundreds of loc…
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Hello,
I'm working with a mixture of low (5-10x) and very low (0.5x) coverage WGS sequences. I've got about 900 of them from a diverse set of populations, and variants are discovered every 10-20bp. I…
nreid updated
4 years ago