Problem while calling copynumber variants using VarScan
Hello, I'm using varscan2 to call copy number variants. But I'm not able to get the raw copy number file. Below is my commands:
$ samtools mpileup -q 1 -f /home/././hg19.fa /home/././Normal.recal.bam /home/././Tumor.recal.bam | java -jar /home/././VarScan.v2.3.9.jar copynumber varscan --mpileup 1
[mpileup] 2 samples in 2 input files
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Reading input from STDIN
Reading mpileup input...
packet_write_wait: Connection to 172.31.1.133 port 22: Broken pipe
TB@X:~$
Please suggest something to solve this problem.
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There is a connection error between your host PC and the remote machine. Nothing to do with VarScan. Are you running this on a cluster? Is there a scheduler such as SLURM? Also check
GNU screento run things in the background.Yeah, I'm running on a cluster. Now, this is solved. I got the raw output file. Thanks. I'm proceeding further.