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Hello,
In large cohorts (~100K) multi-allelic sites are very common. Furthermore, good rare alleles can share the locus of bad, "common" variants (they are common since they seem to appear in many in…
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One major theme raised in #234 is the question of "how do we handle Allele normalization when the Allele Location is specified by Ranges"? To me, these have always seemed to be a shorthand for "I did …
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Hi Jeremiah,
I wonder if you provide example BAM files and output file (.vcf) that I can test svaba and replicate the result. It is because I like to test whether I am running svaba correctly or n…
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In discussions today it was also suggested to amend the current public access feature for multiple levels.
- Access controlled
* The default as it is now
- Fully public
* Corresponding t…
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In the last revision (and perhaps some earlier ones) the option -M in var2vcf_paired.pl doesn't seem to have any effect on the output. I cross-tested the outputs from the new previous tool with an old…
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Are there any plans to implement tumour-only calling, perhaps with a panel of normals as Mutect2 does? I have a batch of tumour FFPE samples with no matched normals that I'd quite like to get Strelka …
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## Background
NGB supports VCF format - users can view VCF-tracks in the Browser, open separate variants to get info, view the full list of variants from the VCF file in the VARIANTS panel.
Curren…
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- [ ] add_value > tools/add_value
- [ ] analyze_covariates > tool_collections/gatk/analyze_covariates
- [ ] annotation_profiler > tools/annotation_profiler
- [x] bamleftalign > tools/freebayes
- [x] b…
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Hi,
I am trying to run openai models on some of the tasks in BBH. I thought cot_fewshot is supposed to be the standard setup with num_fewshot 3. However, when I run `lm_eval --model openai-chat-com…
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**Additional context**
I am trying to apply the soft filter expression from bcbio here on some variant calling data other than GATK.
https://github.com/bcbio/bcbio-nextgen/blob/d27744a4ddcbe35326…