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how to pipe the denovo trio calling? #58

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snijesh opened this issue Jan 13, 2021 · 0 comments
Closed

how to pipe the denovo trio calling? #58

snijesh opened this issue Jan 13, 2021 · 0 comments

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@snijesh
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snijesh commented Jan 13, 2021

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

@snijesh snijesh closed this as completed Jan 13, 2021
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