As all suggested,Read the file and put that contents into buffer 
open FILE,"< generatedFile.txt" or die "cant able to read file

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or

@output = `/home/.../samtools view...`
@fileout = `cat file.txt 2>&1`;

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This works only in unix

In reply to Re: Running an external command by icoder
in thread Running an external command by Eldan Aranye

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