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I simulated the example.vcf file format and split a phased VCF file into VCF file containing two haplotypes (CHR like 3L 3R) by my own python script. I made sure the haplotype VCF file can be processe…
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The naive diploid Viterbi algorithm doesn't scale well with the number of reference haplotypes, slowing testing (#65). @astheeggeggs suggested an alternative implementation that "merges" partial ances…
szhan updated
5 months ago
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Hi,
I just wanted to clarify my understanding of the haplotypes produced in Hi-C mode.
Based on the paper and the docs, my interpretation of the hap1/hap2 output files when both HiFi and Hi-C …
a-lud updated
2 years ago
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Hi,
I want compared the difference between two haplotypes. Can chromap directly alignment two haplotypes? If I want to get alignmet files of two haplotypes precisely. How to get it?
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Hi,
Thank you for this great tool and for diligently answering questions here. If I understand correctly, TRGT only considers reads in the analysis that span the entire repeat region. It therefore …
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Hi, I wondered whether GALA is suitable/capable for keeping and improving haplotigs of the assembly? I've sequenced a triploid species, and would like to phase the haplotypes, no sure if GALA could he…
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Hi Olivier,
I want to use shapeit4 for a small genomic region phasing (300Kbp). Is there something I should be careful for such task? for example the minimum genome requirement, or parameter setti…
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(from @fubar2)
# TreeValGal/EBPhib workflows: October 9 status
### 1\. Current state:
* Two workflows that could be combined into one.
* Need a new name
* Both running on EU and on VG…
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Hey Zachary,
I'm hoping you can help me think through an analysis I'm working on. I have two populations, which we can assume are panmictic. I have run cross-population stats (e.g., XP-nSL, Fst) an…
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Migrate over the genotype plotting functions from anhima.