Problem while calling copynumber variants using VarScan

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4.5 years ago

tanbiswas6 ▴ 10

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.

CNV_VarScan • 763 views

ADD COMMENT • link 4.5 years ago by tanbiswas6 ▴ 10

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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 screen to run things in the background.

ADD REPLY • link 4.5 years ago by ATpoint 82k

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Yeah, I'm running on a cluster. Now, this is solved. I got the raw output file. Thanks. I'm proceeding further.

ADD REPLY • link 4.5 years ago by tanbiswas6 ▴ 10

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