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I have a gzipped file that is too large to unzip and save. I'm looking to use zcat to unzip it and feed it into a java program that takes in multiple inputs. This program has the format:

java -jar GenomeAnalysisTK.jar \
   -T FastaAlternateReferenceMaker \
   -R refgen.fa \
   -o output.fasta \
   -V data.vcf

Where after -V is supposed to be the input from the gzipped file. I've tried something like:

zcat data.vcf.gz | java -jar GenomeAnalysisTK.jar \
   -T FastaAlternateReferenceMaker \
   -R refgen.fa \
   -o output.fasta \
   -V

But this does not work. How can I solve this issue?

ghgh
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  • I suspect that the program is expecting a filename for `-V`. If that is the case, you might be able to stream a list of filenames on the command line, but not their contents. What does the documentation say? – bradimus Jul 21 '16 at 19:57
  • I haven't found an answer when I read the documentation. This is the webpage: https://software.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_fasta_FastaAlternateReferenceMaker.php – ghgh Jul 21 '16 at 20:43

0 Answers0