How to pipe samtools mileup with varscan trio caller?
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
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-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
Thanks!!. It has started running. I'll compare the ouputs of both command and verify
Update: The command has run successfully. But, there is difference in the output provided by both steps.
Number of
de novowithout pipe is66where as in pipe it1292.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).