Varscan Somatic...Syntax To Run With Redirect?

Question

[Hmm]

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

Answer 1

[Sean Davis]

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.

[Hmm]

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

Answer 2

[Pierre Lindenbaum]

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

[Hmm]

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!