Comments (3)
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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Related Issues (20)
- Missing filters in VarScan fpfilter output VCF header HOT 1
- Varscan mpileup2cns error: `Input file(s) were not ready for parsing after 100 5-second cycles`.
- 0 had sufficient coverage for comparison HOT 1
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- 2.4.4 "release" is actually source HOT 1
- Strand filter applied when outputting to tabular format but not VCF
- Malformed VCF output
- NumberFormatException in varscan somatic HOT 1
- mpileup2snp do not detect all snps
- Not filtering reverse strand's strand bias
- how to pipe the denovo trio calling?
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- error download jar, corrupt or incomplete HOT 1
- Reads supporting a variant
- log4j
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- filter for pielup2cns not working
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