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Hi,
I'm getting the following error when trying to joint call some gVCF files:
```
[14707] [2023-11-09 18:40:20.654] [GLnexus] [error] mother_snv.g.vcf.gz Invalid: allele is not a DNA sequence (…
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Hi,
I am currently working on identifying clonal types in my DLP library using mitochondrial variants, and I would like to use your runmtclone.py script (referred to as MityBayes in your paper, I b…
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I have built an Oncoprint plot where I am following this part of the documentation https://jokergoo.github.io/ComplexHeatmap-reference/book/oncoprint.html#define-the-alter-fun . Based on one example f…
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Issue by @MaxUlysse, moved from SciLifeLab#666
- [ ] [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
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Sorry, this is not an issue, just a question regarding the difference between picard liftover and your tool.
I recently tried picard's liftover for lifting over from 37 to 38, and I came across t…
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Hi,
The longphase has an option for co-phasing SNVs, and SVs and SNVs with called modifications.
The input for co-phasing is an unphased SNV.vcf, and didn't work with an already phased VCF when I tr…
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Hi @lh3,
I'm building an assembly-based small variant truth set for NA12878, leveraging assemblies from across the CEPH pedigree and validating inheritance patterns in eight third-generation family…
zeeev updated
4 weeks ago
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Ran on sample using command:
```
# ont version code
spectre CNVCaller \
--bin-size 1000 \
--threshhold-quantile 10 \
--dist-proportion 0.3 \
--coverage input-files/ \
--sample-id…
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**Describe the bug**
I'm trying to generate a simulated dataset by using some different references and a configuration file like the one described in the examples of the README, but they both fail wi…
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Whatshap v2.0
Python 3.10.12
installed via conda
running `whatshap stats` on an assembly with low heterozygosity in places gives this error several times:
` phased_snvs_fraction=phased_snvs …