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piping GATK output to stdout
I want to pipe GATK output to standard output.
I am using a command like this (GATK v2.8-1-g932cd3a):
java -Xmx4g -jar GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T CombineVariants -V in1.vcf.gz -V in2.vcf.gz -o /dev/stdout
However, GATK echos the INFO information in the standard output, mixing information that is not meant to end up in a VCF file.
I have also tried the following command line:
java -Xmx4g -jar GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T CombineVariants -V in1.vcf.gz -V in2.vcf.gz -log /dev/stderr -o /dev/stdout
But this only achieves the result to send the INFO information both to standard output and to standard error.
Is there a way to have GATK not use the standard output to communicate information to the user?
I have checked the documentation at http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_CommandLineGATK.html#--log_to_file but I don't understand how I could do this.