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Expected Behavior
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For Bugs:
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### Environment
#### Steps to Reproduce
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### Description
Field import from Breedbase trial through BrAPI v2 address functions, clicking on "sync" for selected trial brings up popup with "Downloading Observations for Study:", followed by the…
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Dear Developer,
I am trying to use NanoCaller on a high coverage (2000x on Microbial genomes) datasets. When I omit the sub-sampling process, the result genotypes all turned to G
##fileformat=VC…
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svtk vcf2bed uses the ALT field to produce the `svtype` column in the output BED file. This means that the `svtype` column includes BND alt alleles and values like INS:ME for MEIs. However, the [curre…
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Hi,
I am trying to use Whatshap to re-genotype variants I have obtained from DeepVariant across thousands of samples. Hence, my input of `whatshap genotype` is a joint VCF for X samples and X long…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/222) by Peter Ebert (Bitbucket: [ptrebert](https://bitbucket.org/ptrebert), GitHub: [ptrebert](https://github.com/ptrebert)).**
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Dear Hannes
Thank you so much for developing such a nice program.
I used GraphTyper on Manta and CNVnator outputs (after getting the union of SVs by svimmer) successfully. However, when running …
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Hi GATK team,
I wonder if there are some parameters to only genotype a given genomic locus (many locos in bed format), i think this will accelerate the genotyping process instead of genotyping the …
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Good morning, I wanted to ask for some guidance regarding an issue I've been running into while genotyping structural variants using graphtyper. I am attempting a test-run of graphtyper v2 on multiple…
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Dear curators,
I tried to dig deeper into the nature research paper ([Bradley et al., 2015](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703848/)). In terms of mixed infection read analysis, the a…