VarScan copynumber outputName about varscan HOT 3 OPEN

Well, adding "-" after copynumber seemingly can solve the problem when reading from pipe. Good. So, updating the Recommended Workflow on the website is the only thing.

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Sorry to mention, I checked that in the version 2.4.0 and 2.4.1.

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Please update the doc and inline help in a newer version than 1.4.3 to include a good example of piping mpilup to the various caller methods.
Each command is a pain when trying to pipe the mpileup to varscan not to mention that this is not clearly explained in the -h help nor in the Curr Protoc paper which for the remaining is a very good tutorial. This tool suite rocks but lacks a good up-to-date tutorial.

my understanding would be (thanks to @mxqian)

# the first '-' receives the pipe, the next argument $2 becomes the output prefix
samtools mpileup -B -f ${REFFILE} ${NORMALBAM} ${TUMORBAM} \
    | java -jar varscan.jar somatic - ${OUTFILE} --mpileup 1

I hope this also applies to other modules like 'copynumber' (now trying)

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