mavis
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bcgsc
Merging, Annotation, Validation, and Illustration of Structural variants
Certain parts of the validate module contains redundant code: For example - count: https://github.com/bcgsc/mavis/blob/develop_v3/src/mavis/validate/align.py#L417 Align_options for BWA-MEM, which doesn't use any additional align parameter. https://github.com/bcgsc/mavis/blob/develop_v3/src/mavis/validate/align.py#L464 These should be removed or...
Addresses issues in https://github.com/bcgsc/mavis/issues/307
## **Overview** From internal testing, [wtdbg2](https://github.com/ruanjue/wtdbg2) (long read SV assembler) performs well for assembly of breakpoints, something that MAVIS must implement. The following changes must be made to integrate [wtdbg2](https://github.com/ruanjue/wtdbg2):...
**Describe the bug** There is an error running the workflow as it is. **To Reproduce** Built the docker image using Docker file provided with no errors. Downloaded the tutorial data...
Hg38 will remain the workhorse genome for annotation work, but in case users are interested in working with CHM13-T2T in the future - there should be a feature that converts...
Add an optional compression step (default true) to MAVIS outputs since MAVIS can output a lot of files
Hello! I am using Straglr (https://github.com/bcgsc/straglr) for analysis long-read sequencing tandem repeats. The output of the tool is .tsv and .bed . I wanted to annotate the .tsv. The .bed...
Sometimes gene fusion products are far away from the spliced sites. In the future, it would be ideal if MAVIS could integrate transcriptomic data with the fusion calls with genomics...
Currently, a call with: `chr1: chr2 bp1_start: 79836749 IMPRECISE SVTYPE=DEL SVLEN=-28364; ND=79865113 CIPOS=-29,29 CILEN=-53635,53635 ` is being improperly converted to a BPP(Breakpoint(2:79836720-79836778R), Breakpoint(2:79851791-79852493L)
## **Overview** Currently, the Summary module takes in a tab delimited file (similar to a `.bed` file) as the input. For future iterations, we want to change it to a...