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Hi, I want to make sure that when I use smoove call for tumor/normal pairs.
Is there a requirement for the order of two bam files?
Which command is correct ?
The command is as follows:
`smoove ca…
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In the genotypes repertoire [init function](https://github.com/adaptive-intelligent-robotics/QDax/blob/2c7f1b3161b5a7a82148f35f8c231d8a521c5aa9/qdax/core/containers/ga_repertoire.py#L178), a all-zero …
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Can you share the processed genotype and phenotype data?
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Greetings!
Do you have any plans on implementing the genotyping of the variants? Or if you recommend tool that could genotype the VCF output of nanomonsv.
Cheers!
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Hello,
I came across your tool/paper and found it really useful for our research. I was wondering if seGMM could also be used with imputed genotype array data? From what I understand, your focus h…
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Hello,
I am trying to run hisatgenotype. I installed both hisat2/2.2.1 and hisatgenotype. Here's my exact command:
```
python3 /cluster/home/user/hisatgenotype/hisatgenotype --base hla --locus-li…
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```
ds = sg.simulate_genotype_call_dataset(n_variant=2, n_sample=4, missing_pct=0, phased=True, seed=1)
for i, alleles in enumerate(ds['variant_allele'].values):
print(f"Site {i}: {alleles}")
…
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We have a dataset consisting of 4 different genotypes. While we are able to use this package to identify DE genes and their patterns for each genotype individually, we were wondering if there is a way…
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Can you clarify the following: `indel_header.addFormatField("GQ", "1","String", "Genotype quality (currently not supported. Always 0)");`
There are non-zero GQ values in the final VCFs. I am confus…