Question: ChrM in the Varscan2 copynumber output
0
gravatar for lhaiyan3
3.7 years ago by
lhaiyan330
United States
lhaiyan330 wrote:

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 • 1.2k views
ADD COMMENTlink written 3.7 years ago by lhaiyan330

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 REPLYlink written 3.1 years ago by WouterDeCoster42k

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 REPLYlink written 3.0 years ago by lhaiyan330

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

ADD REPLYlink written 3.0 years ago by WouterDeCoster42k

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

ADD REPLYlink written 3.0 years ago by lhaiyan330
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 899 users visited in the last hour