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Hi,
I have been using pbsim3 to simulate HiFi read data and reassemble it to get acquainted with long read assembly. An issue I encountered is the relative cleanness of the simulated data. I used t…
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Something like
```
def individual_heterozygosity(ts, ind):
ts.pairwise_diversity(ind.nodes)
```
should do it - very simple, but we want to make it easy and natural for people to deal with indi…
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Can you briefly describe how KAT calculates the heterozygosity rate reported in the json file?
For one of my genome assemblies, the heterozygosity rate =0, but I believe that is an artifact of the hi…
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Hi there,
I am using GenomeScope2 to check the heterozygosity rate of a plant genome (2n=28) with HiFi reads.
The initial assembly with Hifiasm was used for running a mummerplot with A. thalian…
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Hello, I used Jellyfish to assemble the histogram plot that I plugged into the GenomeScope2 interface. This work is being done on a diploid crayfish genome. I need help interpreting the very slanted n…
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Hello,
Sorry for the question that may seem obvious to everyone else. The software reports 2.5% heterozygosity for my sample. Does this mean I have 1 base every 40 that is heterozygous?
It seem…
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New subcommand to identify regions with heterozygous bases. Should be some type of multimodal versus unimodal test. Will also have to filter out off-by-one regions, maybe by offset testing.
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It would be helpful to calculate genomic intervals and total genomic content of absence of heterozygosity
(AOH)/ Runs of homozygosity (ROH) in consanguineous individuals from the ES-data.
The Lub…
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Uniparental disomy.
We have a graph but it's not great.
What do people want? A list of LOH regions? Node for it?
Report out as BED file etc.
Frank has already incorporated into pipeline.
Peer is …
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My results are giving higher heterozygosity that I expected. I am working with a selfing plant species (rice). I am genotyping with the population genotyper method in the lumpy pipeline (svtyper). All…