Joseph Lalli
Joseph Lalli
I'm working on a custom way to decode sequences using the v3 model. Parts of my sequence are degenerate bases, and I'd like to use the bases on either side...
If I have kmer counts stored as kff files, is there a convenient method to convert them to jellyfish format? Or do I need to recount kmers with jellyfish?
For more background see https://github.com/eblerjana/pangenie/issues/62. Long story short, I'm trying to replicate and make use of the personalized pangenome pipeline described in your recent paper (https://www.biorxiv.org/content/10.1101/2023.12.13.571553v2.full). When using Pangenie to...
Hi there, I'm looking for a good method to combine calls produced by short variant callers (50bp). Most structural variant merging tools are designed to merge SVs from different SV...
*Briefly* looking through the code here, it seems like the basic algorithm (correlation + bootstrapping) is extendable to more than two conditions. This would in effect turn your DE software...
When handling multiallelic sites, the best practice is to split multiallelic sites before phasing. However, I'm not sure how to handle these sites when measuring switch error rate. The posted...
Hello, As an experiment, I've tried take the vcf of the draft human pangenome, use bcftools +setGT to unphase the pangenome vcf, and then rephase the vcf using different reference...
Hi there, I just want to clarify something about the algorithm. When not using a reference panel, does SHAPEIT5 only draw haplotypes from samples that are shared between the scaffold...
Hi there, Thank you for this excellent tool. I'm trying to use it to genotype VNTRs in a diverse panel of WGS samples. I am able to use danbing-tk to...
See https://github.com/MultiQC/MultiQC/issues/2687 and https://github.com/MultiQC/MultiQC/pull/2690