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Hello, I have 11 samples from 1 patient so I am trying to run an nd analysis. I ran this successfully on 3 samples but when I increase, when "Estimating density for all MCMC iterations..." the vector …
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When calling create we are doing quite a lot of API calls (see analysis in #17). Look into ways of reducing the number of calls.
* Perhaps, using GraphQL mutations (if supported by GitHub) can wor…
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**Motivation**: There are many steps within _breseq_ that could be easily parallelized to speed up execution.
**Implementation**: Use a thread pool that relies only on C++11 std:thread to maximize …
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Seen in https://jenkins.scylladb.com/view/master/job/scylla-master/job/dtest-debug-random/521/artifact/logs-all.debug.2/1626560947253_lwt_schema_modification_test.LWTSchemaModificationTester.index_dro…
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Link to the tutorial is below. Under the sub-heading "Identifying Candidate Mutations: Variant annotation." The version of the SnpEff tool required for the Hand-on is 4.1.0. I tried my hands on the tu…
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It would be nice to be able to constrain which tests get run based on coverage analysis. That is, when a change is made, determine what gets changed and only apply mutation to that section. Moreover, …
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1. Sometimes after running AA and getting ecDNAs, we also want to find some somatic mutations or allele-based CNA and so on, so the RG tag in bam is mostly important ! In order to reuse the bam file f…
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This is a feature request or, alternatively, a request for advice.
The ability of breseq to compare different samples in an HTML file is super useful. I am wondering how to use that information for…
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| --- | --- |
| Bugzilla Link | [341944](https://bugs.eclipse.org/bugs/show_bug.cgi?id=341944) |
| Status | NEW |
| Importance | P3 enhancement |
| Reported | Apr 05, 2011 12:34 EDT |
| Modified …
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Hi!
I ran the RUNNER pipeline code, but I only got the excel file of variant annotations, with no qqplot, no *.gene.mutationburden.txt, which is described in https://pmglab.top/kggseq/doc10/UserMan…