Question: How to pipe samtools mileup with varscan trio caller?
6
gravatar for dare_devil
14 days ago by
dare_devil1.3k
India
dare_devil1.3k wrote:

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
pipe samtools varscan • 82 views
ADD COMMENTlink modified 14 days ago • written 14 days ago by dare_devil1.3k
2

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.

samtools mpileup -B -q 1 \
     -f ref.fasta \
     dad.bam mom.bam child.bam | varsan trio - trio.mpileuup.output....

More relevant reading: https://unix.stackexchange.com/questions/16357/usage-of-dash-in-place-of-a-filename

ADD REPLYlink modified 14 days ago • written 14 days ago by _r_am32k
1

Update: The command has run successfully. But, there is difference in the output provided by both steps.

Number of de novo without pipe is 66 where as in pipe it 1292.

ADD REPLYlink written 13 days ago by dare_devil1.3k
1

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).

ADD REPLYlink written 12 days ago by _r_am32k

Thanks!!. It has started running. I'll compare the ouputs of both command and verify

ADD REPLYlink written 14 days ago by dare_devil1.3k
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