ChrM in the Varscan2 copynumber output

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8.1 years ago

lhaiyan3 ▴ 80

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

varscan2 copy number • 1.9k views

ADD COMMENT • link 8.1 years ago by lhaiyan3 ▴ 80

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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 idxstats on the bam file and grep '>' on the reference fasta.

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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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.

ADD REPLY • link 7.3 years ago by lhaiyan3 ▴ 80

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You mean the chromosomes are not in the same order in both files?

ADD REPLY • link 7.3 years ago by WouterDeCoster 47k

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No, they are in the same order in both files. I mean chrM is the first in both files.

ADD REPLY • link 7.3 years ago by lhaiyan3 ▴ 80

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