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` ?

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