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One genotyping vendor types HLA using RT PCR / Taqman approach. It seems similar to SSP, and that can work in this case, but if there are future HML versions maybe we discuss if this is needed.
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Hi,
I used GAPIT few months ago and it worked perfectly, Now i ran GAPIT functions after getting new data and these errors pops out. I tried using the old data as it is, but same happens. Please H…
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```
ds = sg.simulate_genotype_call_dataset(n_variant=2, n_sample=4, missing_pct=0, phased=True, seed=1)
for i, alleles in enumerate(ds['variant_allele'].values):
print(f"Site {i}: {alleles}")
…
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Hello,
Thank you for this tool! Your paper on PRDM9 Allelic Variation is quite interesting. I also have some samples sequenced on PacBio. And I was wondering if you have a version of this script th…
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Hello, I am new to this analysis, I would like to know how you can match your patient's genotype with its phenotype, can you please load up the code?
Thanks so much
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Hey Brent,
I've been testing this out recently and I really love how fast it adds the annotations. I have a particular use case, and it may be something you don't want to support, but I thought I wou…
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The allel.stats.decomposition.pca function does not allow for missing data in the genotypes array. If I build the geno array using geno = genotypes.to_n_alt() it will work, but with geno = genotypes.t…
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I was wondering whether it is likely that you will ever introduce a feature allowing data to be inputted in genotype likelihood format, in addition to hard genotype calls? This would be very useful in…
sahwa updated
5 years ago
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In line 235, the threshold to call genotype is hard-coded to 98%. Could you add an input variable that can customize this?
https://github.com/USDA-VS/GenoFLU/blob/f08f571336d37e2667d1dff6896fb47db0…
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Can graphtyper output the genotyping of all sites in a region, such as mitochondrial 16569bp?
```shell
./graphtyper genotype ~/data1/References/human/Homo_sapiens_assembly38.fasta --sam=~/data1/pr…