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I've been trying to run BayesTyper on a VCF file ([uploaded here](https://gist.github.com/Parsoa/1e5407b6f45ab54a6736f7d8a234fa1f) which is basically the merged set of calls from HG00514 and HG00733 f…
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Hi,
Thank you for developing this tool which is quite easy to use!
I am wondering if SpecHLA could also be used to detect somatic HLA mutations since we have paired tumor and normal WES or RNA…
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# Association
- [ ] [A simple, consistent estimator of heritability for genome-wide association studies]( https://www.biorxiv.org/content/biorxiv/early/2017/10/17/204446.full.pdf)
- [x] [Multivari…
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```javascript
// We want to run a bunch of variant callers
// Then count common SNPs
const variantCallerInput = {
reference: '*_genomic.fna',
bam: '*.bam',
_bai: '*.bam.bai'
}
// two…
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We had some discussion in the @Clinical-Genomics/rare-disease team and we find the filename `managed_variants.vcf` to be somewhat confusing. The file name is ambiguous as it is not clear whether thes…
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Dear CliqueSNV team,
I've been experimenting with your tool and think perhaps I have found a bug. If there is a single, isolated SNV with no other SNVs in linkage within the mapping reads, i.e. dis…
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Hi @Cloufield
I'm having a weird error while performing liftover that I cannot explain.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "src/liftover/chain…
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The evidence record currently only supports an evidence type and text description. Are there advanced plans to extend this?
In other parts of the API a metadata key-value pair structure is used to al…
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**Describe the issue:**
Thank you so much for the great tool.
I'm working on a heterozygous mouse long-read RNA-seq dataset from PacBio and would like to perform variant call + phasing at read-le…
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Hello, I would like to ask for the implementation of a SlidingWindowWalker (both for reads and variants), that could be very interesting for other tools. I was thinking that it could be similar to Int…