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Varscan Somatic...Syntax To Run With Redirect?

i am running a java inside my perl code. As follows: Varscan somatic takes 2 parameters. Each parameter is an executable line by itself which gives an output. That output is used as an input for the varscan somatic java part. I am doing the following: 

$n_p = "samtools view -b -u -q 1 $n_b | samtools pileup -f $r -";
$t_p = "samtools view -b -u -q 1 $t_b | samtools pileup -f $r -";

bash -c \"java -jar VarScan.v2.2.jar somatic <\($n_p\) <\($t_p\) output

I am running the code on a unix machine.The above code gives me error. i want the $n_p and $t_p output to be fed into the java.

Does anybody have a comment as to what the correct syntax is.

Thanks

varscan samtools
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updated by Biostar Biostar • written by Hmm • Hmm

2 answers

You'll need to modify the absolute paths, etc., but I use little shell script takes the parameters from the command line and uses fifos (named pipes) to eliminate the need to make large pileup files. The script is here.

• 86 views • link
written by Sean Davis Sean Davis

excellent...this seems to be working....i will keep you posted..!

• 25 views • link
written by Hmm • Hmm

try:

samtools view -b -u -q 1 $n_b | samtools pileup -f $r - >  normal.pileup
samtools view -b -u -q 1 $t_b | samtools pileup -f $r - >  tumor.pileup
java -jar VarScan.v2.2.jar somatic normal.pileup  tumor.pileup output
• 2 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

This approach will create 2 massive pileup and when i am running the java part..the process is killed ,i guess becasue of I/O..etc. Any suggestions!

• 1 views • link
written by Hmm • Hmm

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