Entering edit mode
2.2 years ago
dare_devil ★ 1.7k
I have seen piping samtools with varscan as follows
samtools mpileup -f reference.fasta sample1.bam sample2.bam | java -jar VarScan.jar mpileup2snp
But how to pipe the following pipeline for varscan trio
#Generate 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 \ #this is input trio.mpileup.output \ #this is output --min-coverage 10 --min-var-freq 0.20 --p-value 0.05 \ -adj-var-freq 0.05 -adj-p-value 0.15
A lot of tools allow for
-to stand in for STDIN. I'm not sure of this, but I think it's a shell feature. Try that.
More relevant reading: https://unix.stackexchange.com/questions/16357/usage-of-dash-in-place-of-a-filename
Update: The command has run successfully. But, there is difference in the output provided by both steps.
de novowithout pipe is
66where as in pipe it
That's odd. Maybe open an issue/talk to varscan developers? You may want to dig deeper and see what's unique about the 66 captured - maybe they're closer together on the pileup output (I'm just going with a wild guess).
Thanks!!. It has started running. I'll compare the ouputs of both command and verify