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
Do you have R installed (and
Thanks for your response. Yes I have R and argparse package installed.
Using your suggested command outputs the error:
I have write and execute permissions to this directory.
Your command line must have an incorrect option. Can you provide your command line (obfuscate any real names if you want).
This is the code I ran: