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Hello, thank you very much for your SubPhaser software, which is very useful for genotyping. I used HIFI and HIC to assemble the genome of Fragaria x ananassa but I do not know the homology of the 28 …
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From Daniil (#22):
> Use a neural network that is trained on a real dataset, then inject SNPs and phenotypes. In that way, you should detect if the neural network pick it up yes/no
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I'm trying to use the profile_AA_x0 function of the R package 'Genogeographer'. It has the following usage description:
**Usage**
profile_AA_x0 (AA_profile, df, select = c("locus", "x0"), keep_…
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- better description of creation of genotype frequency files.
- add description of how to run merge step
- fix `${PWD}` case in readme
- consider handling of missing files/samples
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I've been trying to run BayesTyper on a VCF file ([uploaded here](https://gist.github.com/Parsoa/1e5407b6f45ab54a6736f7d8a234fa1f) which is basically the merged set of calls from HG00514 and HG00733 f…
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Hi,
Thanks for developing such an interesting tool, that could make the difference in the application of conservation genetics ! I wish I will be available to run feems on my dataset.
Could you pl…
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Multi-allelic variants where introduced in #17 by adding a new `List` with the secondary alternates. This approach has some problems for mixtures of SNPs and INDELs when the normalization changes the …
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Dear author,
I met a problem that shows the diffs matrix is not full rank. Because my snps matrix only included the mtDNA bi-allelic SNPs, and they were just converted into the 0|0 or 1|1 format, I…
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- [x] Subset genoype data into AMR-detected, no AMR detected
- [x] Group samples with same AMR genes
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Notes for the meeting with Dr. Mcpharland.