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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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Hello,
I noticed that Clair3 is not calling a variant near the end of a short reference sequence (position 2265 of Influenza A virus PB2 sequence [OP597571.1](https://www.ncbi.nlm.nih.gov/nuccore/O…
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I have a scRNAseq samples SORTseq protocol, well plate based, I have this error when I do the run_numbat, my script only gets to do the hierarchical clustering, but then it stops, I have tried with di…
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Thank you for creating this valuable tool. We've found it to be the best for analyzing our data compared to other tools, but we've noticed a discrepancy in genotyping the KIR2DL5A/B genes. While other…
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**1. What were you trying to do?**
I tried to perform vg construct on each chromosome
```vg construct -C -S -R ${chrs[SLURM_ARRAY_TASK_ID]} -r $ref -v ${split_chrs}/${chrs[SLURM_ARRAY_TASK_ID]}_…
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Hello
I am looking at adding GRIDSS to parliament, but it appears that survivor does not support GRIDSS output. AFAIK, GRIDSS is fully compliant with VCFv4.3 but there are a number of issues I've e…
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>>
>> https://github.com/rmcolq/pandora/blob/815da22867f2bdaa3e3bf40f382be830c1506b0a/src/estimate_parameters.cpp#L217-L231
>>
>> In particular https://github.com/rmcolq/pandora/blob/815da22867f2…
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Hi Joelle,
I was trying to run some gene-based tests on an unbalanced (398 cases and 401739 controls, so roughly 1:1000) binary trait (either `spa` adjusted or `firth` / `approx` flags). However, …
Ojami updated
2 years ago
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In your vignette you state that: "Pre-computed [marker maps] for the MUGA series of arrays are available from [URL]."
What is the URL for downloading the marker map file?
Thanks!
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Many existing pipelines implement features from GATK/VQSR to distinguish between true and false de novo mutations. Given GLnexus variant calling, these pipelines cannot be adapted.
Do you have rec…