Test-drive the GATK tools and Best Practices pipelines on Terra
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GenotypeGVCFs: stand_emit_conf not defined
Hi, I got an error from GenotypeGVCF that says the argument stand_emit_conf is not defined, while the documentation of GenotypeGVCF has that option.
Here is the command line I used. I am using GATK 3.6, I tried the 9/7, 9/26, 9/27 nightly builds and they gave me the same error.
$ ~/bin/java-1.8.0/bin/java -Xmx2g -jar ~/bin/GenomeAnalysisTK.jar -T GenotypeGVCFs -R ~/ref/hs37d5.fa -V samples135.20.g.vcf -o samples135.20.vcf -stand_call_conf 5.0 -stand_emit_conf 5.0 -inputPrior 0.0010 -inputPrior 0.4995 -A GCContent -A BaseCounts