How to pipe deovo trio with samtool mpileup?

[snijesh]

Running trios pipeline

#Create a three-sample mpileup
samtools mpileup -B -q 1 \
-f ref.fasta \
dad.bam mom.bam child.bam >trio.mpileup

#Run VarScan trio
varscan trio trio.mpileup trio.mpileup.output \
      --min-coverage 10 --min-var-freq 0.20 --p-value 0.05 \ 
      -adj-var-freq 0.05 -adj-p-value 0.15

Is it fine to pipe the command as follows: samtools mpileup -B -q 1 -f ref.fasta dad.bam mom.bam child.bam | varscan trio - trio.mpileup.output --min-coverage 10 --min-var-freq 0.20 --p-value 0.05 -adj-var-freq 0.05 -adj-p-value 0.15

[mkohailan]

I tried it before and it worked for me

samtools mpileup -B -q 1 -f ref Father.bam Mother.bam Child.bam | java -jar VarScan.v2.3.9.jar trio --output-vcf output_file