Question

I want to run the following code inside a bash script:

java -jar VarScan.v2.2.jar somatic < samtools view -b -u -q 1 $n_b \
| samtools pileup -f $r - < samtools view -b -u -q 1 $t_b \
| samtools pileup -f $r - output

where $n_b and $t_b are files.

The java somatic function takes 2 paramters. so

samtools view -b -u -q 1 $n_b | samtools pileup -f $r

is one of the parameters and

samtools view -b -u -q 1 $t_b | samtools pileup -f $r

is the other paramter. Both the parameters are executable themselves.

So what i want is

samtools view -b -u -q 1 $n_b | samtools pileup -f $r -

execute first then

samtools view -b -u -q 1 $t_b | samtools pileup -f $r

and the output becomes the input for the somatic.

Answer 1

The solution to my question is found at:

https://gist.github.com/1022747