Ye Tian

Update: problem soved. the parameter --mpileup 1 has to be added into the command. This was mentioned within the manual but not the protocol article. This is really basic. I was following the instructions from the protocol Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection I have a pair of normal tumor samples to analyze so I followed the instruction to mpileup them together with samtools. A combined, mpileup'ed file was generated. However, when I called the function VarScan...

This is really basic. I was following the instructions from the protocol Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection I have a pair of normal tumor samples to analyze so I followed the instruction to mpileup them together with samtools. A combined, mpileup'ed file was generated. However, when I called the function VarScan somatic, I put in one input, followed by the name of my designated output filename. I keep getting error notice that I finally figured out it's expecting...