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seGMM failed to proceed with plink with an error,
```
>> Collected feature of X chromosome heterozygosity
When running: plink --vcf HG002.vcf --make-bed --out test_seGMM/plink
An error was occur…
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Hi, Thank you for creating Sim-it. I enjoyed your benchmarking paper and I have been trying to run Sim-it. I am trying to run it on a single chromosome (26 Mb). I have tried running it with the defaul…
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Having shown GosCan to some people who haven't seen before, I have heard requests to add legends and remove abbreviations.
In the linear view:
CNV -> copy number variants
LOH -> loss of heterozyg…
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Hello!
Our group is attempting to generate collapsed assemblies for multiple species. We have a method to do the error correction ourselves and reduce heterozygosity quite a bit. Are there parameter…
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Hello, I was curious about some Issues that I have encountered.
1. Using pseudohaploid individual on the pop1 of f3 results into NA.
When the population 1 is only one individual and is pseudohaplo…
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Hello, thanks a lot for the great assembler.
I used hifiasm to assmbly three different heterozygous insect genomes using the option "-l 3". For the most heterozygous species I got a big circular sc…
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Hello, sorry this is a duplicate, but I don't know if you see when someone comments on a closed issue:
https://github.com/KolmogorovLab/hapdup/issues/18
Also, the solution is not really explicit,…
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Hi,
I am trying to use genomescope to estimate heterozygosity and genome size of a fairly large plant genome, ~ 3.65Gbp. I am using the histogram of canu-corrected reads. Here is what I am getting:…
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Hi,
How to convert vcf format to lfmm genotype format? How to deal with heterozygosity and missing data in vcf? I can only see 0 and 1 in example data.
Best wishes,
Kun
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I run IQ-Tree multicore version 2.1.3 COVID-edition for Linux 64-bit built Apr 21 2021 with the following cmd:
iqtree2 -s used_outgrp.flt.snp.pop.cf -m GTR+P -nt AUTO -ntmax 14 -bb 1000
And I got th…