Calling triovariants using varscan from a compressed mileup file ?
1
6
Entering edit mode
9 months ago
dare_devil ★ 1.5k

I used following commands to call denovo variants from 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 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

But, here the output generated from mpileup is really huge. Are there any ways to feed compressed files to the varscan trio ?

varscan samtools trio mpileup pipe • 275 views
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3
Entering edit mode
9 months ago
svp ▴ 450

You can try: < zcat (file.gz) as input

varscan trio < (zcat trio.mileup.gz) 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
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