Hi. I have been running VarScan2 copynumber
according to the manual's instructions, shown here:
My exact command is:
The problem is that it is not writing the output to my file "tumor.copynumber" but instead to "output.copynumber" which is the default. Anyone have any idea why?
according to the manual's instructions, shown here:
samtools mpileup -q 1 -f ref.fa normal.bam tumor.bam |
java -jar VarScan.jar copynumber varScan --mpileup 1
This will create a single output file, varScan.copynumber, containing the raw copynumber calls.
java -jar VarScan.jar copynumber varScan --mpileup 1
This will create a single output file, varScan.copynumber, containing the raw copynumber calls.
My exact command is:
samtools mpileup -B -q 10 -f genome.fa normal.bam tumor.bam |\
awk -F"\t" '$4 > 0 && $7 >0' | java -jar $varscan_dir/VarScan.jar copynumber \
tumor.copynumber --mpileup 1 --data-ratio 0.50
awk -F"\t" '$4 > 0 && $7 >0' | java -jar $varscan_dir/VarScan.jar copynumber \
tumor.copynumber --mpileup 1 --data-ratio 0.50
The problem is that it is not writing the output to my file "tumor.copynumber" but instead to "output.copynumber" which is the default. Anyone have any idea why?
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