ChrM in the Varscan2 copynumber output
Hi,
I am using the varscan2 to call the copynumber for the WES. But my output.copynumber file just has the chrM call. I used the following script, can anyone please give me some suggestions? Thanks very much. HY
samtools mpileup -q 1 -f $ref normal.bam tumor.bam | java -jar $VARSCANHOME/varscan.jar copynumber varScan --mpileup 1
java -Xmx64g -jar $VARSCANHOME/varscan.jar copyCaller output.copynumber --output-file output.copynumber.called
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Do the chromosomes specified in $ref correspond to those in the bam file? Easiest way to check this would be to run
samtools idxstatson the bam file andgrep '>'on the reference fasta.I tried both, I have the chrM to chrY in the bam file and ref file, but the chrM is the first, it looks like the program stopped after running the chrM.
You mean the chromosomes are not in the same order in both files?
No, they are in the same order in both files. I mean chrM is the first in both files.