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Hi,
I am working with HIFI+HiC haplotype resolved assembly with HIFIasm (both have been also scaffolded with HiC data). Based on BUSCO and Merqury results, assemblies contain ~%3-4 duplication. I w…
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Hi,
I have been using RFmix for a while and it works really well. Just a quick question, in the output file, we will have samplename.1 and samplename.2 for haplotypes at one site. How does the resu…
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### Description of feature
**feature requirement**
Phasing assessment is required for phased assemblies. A heatmap generated from combined haps can assist with this checking. This is required for re…
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Hi @dfguan,
Thanks for the excellent tool.
I am trying to scaffold two separate phased haplotype assemblies of the same diploid plant genome (assembled with HIFIasm). Since I am using the same …
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I hope this message finds you well. I am currently working with Cactus and have a specific question regarding the analysis of differences between two haplotypes. Specifically, I am interested in ident…
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I am getting the above error even though the region is present in my data. What could be wrong?
```bash
./LDBlockShow-1.40/bin/LDBlockShow -InVCF haplotype_gene_quantification/g3_variants/haptags_…
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Hello Dr. Rannala,
Is there any reason I should not use the haplotypes of RADseq loci in BA3SNP as long as I filter for
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### Need
As a user, I want clear outputs. At the moment variant files are a mix of vcf and bcf, some indexed and some not, some compressed and some not.
### Suggested approach
Standardise output va…
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First of all, I'd like to thank you for the amazing work done!
Secondly, I'm working on a fungal species with very high levels of chromosomal polymorphism and large translocations (of Mbp), and I alr…
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My reference panel has 1600 individuals and 4368645 variants. When imputationin the BAM file of 82 1x depth individuals, I found that the imputation speed was very slow. I also changed -- rare_af_thre…