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Code Block
titleCreate the "commands" file to run annovar on six vcf files - use Perl to extract the sample name and mapper so the log files have meaningful, but shorter, names
ls *.vcf | \
  perl -n -e 'chomp; $_=~/(NA\d+).*(sam|GATK)/; print "annovarPipe.sh $_ hg19_annovar_db >$1.$2.log 2>&1 &\n";' > commands

Note how the print statement includes redirections for generating log files, and the entire output is redirected to a file named commands.

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