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rbronste
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@rbronste-12189
Last seen 5.0 years ago
Hi
Using a package that requires samtools and only finding Rsamtools from Bioconductor, have that loaded and getting the following error:
sh: samtools: command not found
Error in readBAMIndex(bamFile, refgenome = refgenome) :
Cannot run "samtools". Install "samtools" first!
Is there a regular samtools package? Having trouble locating it. Thank you.
I realize that this is a long shot, but did you ever find a fix to this? I'm getting the same error but samtools seems to be installed correctly. I can run it in terminal but R can't find it.
Cheers
The original answer still applies. If the package you are trying to use -- which package? -- requires the samtools application to be installed (and discoverable, so somewhere in specified by the PATH environment variable) then you'll need to install samtools independently of R. If you need help doing that, then probably you need to ask somewhere (biostars?) where there is more likely to be relevant expertise.
Alternatively, if you're trying to access or manipulate BAM files from within R, you might try the Rsamtools or GenomicAlignments (or VariantAnnotation, for VCF) packages.