Manavalan Gajapathy
Manavalan Gajapathy
Hovering doesn't work anymore on coverage plots. Tested on mac and firefox/chrome. Solution: Debugged a bit and narrowed down the issue to plotly version used in URL `https://cdn.plot.ly/plotly-latest.min.js`. Hovering works...
I tried out AnnotSV v3.0.4 for about 20 samples, and none of their SVs are scored rank-2 in `ACMG_class` column. Here is an ranks for one of the WGS samples:...
I think I'm missing something obvious here. Running this pipeline results in output files/directories created in the same directory as `Snakefile`. How do I direct them instead to directory of...
What singularity image is used for this pipeline? Repo's readme says this pipeline can be run with singularity, but I don't see [`singularity:` defined](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#combining-conda-package-management-with-containers) anywhere in the pipeline.
Svtools' `vcftobedpe` tool produces one-based START coordinates in bedpe output, instead of [zero-based coordinates that bedpe requires](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format). I came across this (major) bug as [bedtools' pairtopair](https://bedtools.readthedocs.io/en/latest/content/tools/pairtopair.html) would not work as...
SimGIC score calculated using FastOwlSim doesn't match among output files written in FORMATTED and CSV formats. However, SimGIC calculated using SimpleOwlSim matches with that calculated using FastOwlSim in output format...
Can VerifyBamID be used to identify the source of contamination? That is, identifying the sample that is contaminating an intended sample. For example, in a project with 100 EUR ancestry...
Hi, I am [working on including support](https://github.com/ManavalanG/MultiQC) for MinIONQC in [MultiQC](https://multiqc.info/), which is a fantastic results aggregator. So far, I have added results using `summary.yaml`; see this html file for...
For this record in input [example bed file](https://github.com/lgmgeo/AnnotSV/blob/master/share/doc/AnnotSV/Example/test.bed) ``` 1 149041933 149209289 DEL Benign ``` [AnnotSV's output](https://raw.githubusercontent.com/lgmgeo/AnnotSV/master/share/doc/AnnotSV/Example/test_GRCh37.annotated.example.tsv) is this (just showing first few columns of the `full` row): ``` 1_149041933_149209289_DEL_1...
**Snakemake version** Tested in v5.9.1 and v5.30.0 **Describe the bug** When snakemake’s `group:` feature is used when pipeline is run in cluster, it seemingly modifies the file modification time of...