I am very new to using FACETS. I was wondering if there is a way to run the Rscript snp-pile-wrapper.R directly on the command line without installing facets using conda or from GitHub. Is this possible? I've tried running this using the following example command provided at https://github.com/mskcc/facets-suite#, substituting the arguments with the actual paths to my files and chosen prefixes:
snp-pileup-wrapper.R \ --snp-pileup-path <path to snp-pileup executable> \ --vcf-file <path to SNP VCF> \ --normal-bam normal.bam \ --tumor-bam tumor.bam \ --output-prefix <prefix for output file, preferrably tumorSample__normalSample>
However, I get the following error:
'snp-pileup-wrapper.R: command not found'
The Rscript is located within the path supplied after