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Does STIX support genotyping of translocations? If so could an example be provided in the README? If not, what would be involved to support translocations and would you be willing to provide advice …
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PacBio CCS reads have a very different error profile to standard PacBio CLRs. Are there suggested HMM settings for genotyping CCS reads, in a context where I do not have access to subreads (even thoug…
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Dear Giovanni,
Thank you for your nice software. I am using scAllele for the detection and analysis of variants using scRNA-seq. I wonder how you get the information about 0/1 or 1/1 in Figure 2E of …
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I am trying to run GONE with 10k and 100k SNPs for a non-human dataset, but seem to be getting the following error.
```
script_GONE.sh: line 71: ((: i
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Can the proposed [/search/variantmatrix](https://app.swaggerhub.com/apis-docs/PlantBreedingAPI/BrAPI-New-Concept-Preview/0.0.0-proposal#/Genotype-Matrix-Redesign/post_search_variantmatrix) endpoint ha…
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Meta-issue. Please spin out issues and self-assign.
For the first cut, let's organize WDLs and resources for a pipeline that takes
**Inputs**
- the joint short-variant callset
- the integrated…
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Suggested by Peter Du, who observed that HaplotypeCaller finds ~3400 snps (~7700 snps + indels) in a mouse exome, vs. ~2000 hets found by CollectAllelicCounts + naive genotyping. See related issues #…
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Hello.
I'm trying to run SCOUT on a single sample I have from a 10X genomics run.
I have run the BAM file through the GATK recalibration steps and try to use SCOUT to call genotypes.
This is th…
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Hello --
Thank you for developing and maintaining a powerful resource for the genomics community.
I've genotyped SVs for a species of bird, and noticed there was an aberrantly large inversion t…
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Hi,
I will be performing trio analysis for SVs. Is there any recommendation for trio analysis using cuteSV (joint genotyping or any tested workflow)? I will be using minimap2 as an aligner.
Rega…