In order to perform somatic mutation calling with varscan, I need to run this line:
java -jar VarScan.jar somatic normal.pileup tumor.pileup output.basename
I was wondering if there is a place to get either a pileup version of hg19 or even a bam file of it in order to put it in the spot for "normal.pileup" as required by the command above. I'd rather download it because going through the process of creating such a file from the fastq file I have will take forever.
Thank you for the explanation, that clears up a lot. Right now I'm working on learning the pipeline to go from the original Illumina sequencing reads (fastq) to a VCF file. I have the two original read files and a copy of hg19, and all the other files I have have been derived from these three files. I'll have to check in with my PI to clarify about getting the control sequencing file.
Is this a whole-genome sequencing experiment and what computational equipment do you have around (CPUs, RAM)?