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Hi @etal, wanted to pick your brain on how to implement some kind of "confidence intervals" around the copy number estimates. Ideally there could be an interval around the point estimate that would re…
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Hi @jrburke, I maintain a few advanced loader extensions based on the previous es6 spec which this seems to take some inspiration from. I'm interested in trying to implement some of these using your …
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In my field of research, it is very common to remove and/or insert custom DNA sequences in microbial genomes. I would like to make the same changes _in silico_ in the FASTA file of the reference genom…
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Would allow for greater custom flexibility, especially for amplicon sequencing where intronic regions are targeted.
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Hi,
When I ran the preprocess command of PyLOH using the bedfile with target regions from exome sequencing, I get the error below. When I remove the bedfile, it runs fine. What could be the issue here…
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The reasoning is simple, depending on the application, the concept of "high" and "low" differ. For example, under what category would exome sequencing and targeted sequencing fall? At the moment it is…
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This occurs with a targeted sequencing dataset:
```
[0:apply]: IndexError: index -31 is out of bounds for axis 0 with size 17
```
This is repeated many times (with a slightly different output). I'm …
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Consider a researcher who writes a script against the GA4GH APIs, accesses data and publishes the results. The current APIs do not guarantee that subsequent researchers will get the same result when r…
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I've reviewed the results produced by both my MuTect code and the generic GATK variant caller and I noticed the presence of regions outside the ones I had specified in the configuration.
Likewise, t…