varCA
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aryarm
Use an ensemble of variant callers to call variants from ATAC-seq data
After preparing the required input, the pipeline can't seem to find the specified files or output directory. I don't see in the log files whether or not my sample file...
I've successfully run the example. I don't understand the output out/merged_snp/jurkat_chr1/final.tsv.gz What is the final call? And is what should I use as the measure of confidence? Thanks.
...to endorse the use of mamba and offer a docker container for those who prefer it (see https://github.com/aryarm/varCA/issues/8#issuecomment-811374035)
**Describe the bug** ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0'. **To Reproduce** Could not create conda environment from /lustre/grp/bitcap/jinxx/source/varCA/rules/../envs/prepare.yml: **Expected behavior** A clear and concise description of what...
Hello, I recently downloaded VarCA to run on my ATAC data. Installation was apparently successful, but upon running "./run.bash &" from within the VarCA directory I get an exit (1)...
scATAC-seq BAM files from CellRanger can be used with VarCA, but there is an important caveat that one should be aware of: **tldr; if you give VarCA BAM files, you...
When running the `prepare` subworkflow, users of VarCA might occasionally run into the following error: ``` $CONDA_PREFIX/lib/R/bin/R: line 238: $CONDA_PREFIX/lib/R/etc/ldpaths: No such file or directory ``` This error can happen...
Hi @aryarm , I am running your pipeline starting with called peaks and a .BAM file. However, when doing a dry-run, I get the following error: > "Building DAG of...
for either the reference genome, the BAM files, or the fasta files we've been depending on the tools in our workflow to handle these errors, but we could also just...
Our current test dataset comprises all of chr1 in two different samples: the Jurkat sample and the MOLT4 cell line. It takes about an hour to run the entire pipeline...