Overview:
The problem with yesterday's SAMtools tutorial was determined to be a rather annoying typo in the mpileup command. Specifically, the SAMtools mpileup -f option is supposed to reference the reference.fasta file that you have previously indexed, NOT the indexed file itself. My most profound apologies for not having caught this quicker when it became clear there was a problem.
Solutions:
- The SNV_tutorial is now fixed on the website and the commands will work as they appear with the output from the bowtie2 mapping tutorial that you completed in class.
- I have created a single text file that you can execute on an idev node (NOT as a commands file submitted to the queue!) This file will execute the entire samtools pipeline that exists within the SNV tutorial in ~7 minutes using the output of the bowtie2 tutorial stored in a permanent directory.