varCA
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aryarm
Use an ensemble of variant callers to call variants from ATAC-seq data
It shouldn't be too hard to comply with [these standards](https://snakemake.github.io/snakemake-workflow-catalog/?rules=true). We just need to add a `.snakemake-workflow-catalog.yml` file and restructure the project folder structure (note, this issue is part of...
The ATAC-seq data we work with is single-end, which is not supported at the moment. Ideally, of course, this feature could be introduced. However, in the meantime, I was wondering...
There are a lot of config options and it might be hard for a user to know how to fill them, despite all of the documentation I've provided. It would...
Our pipeline requires that users install every variant caller at runtime, even if they don't actually use some of them. For example, DELLY is not used by the pipeline by...
At the end of the `prepare` pipeline, a couple of post-processing steps are performed on the merged TSV before we feed it to the `classify` pipeline. All of the scripts...
## The problem @Jaureguy760 discovered that [the `predict_RF.R` script](https://github.com/aryarm/varCA/blob/master/scripts/predict_RF.R) uses an excessive amount of memory (up to ~400 times the size of its input data!). We should investigate why this...
If `channel_priority` is set to `"strict"` in one's `.condarc`, it becomes impossible to install the `prepare.yml` environment file. `conda` will just spit out a bunch of conflicts. Ideally, all of...
Hi , I got the following error: (I added `-set x ; set -e ; set -o pipefail` to view the output of `callers/vardict` I also set `my $sample="";` line...
Many callers output both InDels and SNVs in the same VCF. In order to separate them from each other before outputting to the final TSVs, we use `gatk SelectVariants`. It...
The `classify` pipeline creates [several figures as part of its output](https://github.com/aryam7/varCA/tree/master/rules#output-1). Snakemake has a `report()` function for marking these figures as such. Consider using it. That way, the user could...