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I am running VariantAnnotator and noticed that from the annotation options in the input vcf header, only DP and FS are accepted in the command-line:
java -Xmx100g -jar GenomeAnalysisTK.jar -R /home/gp53/tophat/genome.fa -T VariantAnnotator -I ./input.bam -o ./output-gatk-varannot.vcf --variant ./input-gatk.vcf -A DepthOfCoverage -A FisherStrand --dbsnp ./dbsnp_137.hg19.vcf
Other annotation options like AC, AF are not recognized and VariantAnnotator crashes.
I tried looking for the available options with java -Xmx100g -jar GenomeAnalysisTK.jar -T VariantAnnotator --list, but instead of the list of available annotations, I get the usage.
Also, what are most important annotations to consider in VariantRecalibration? Are DP and FS good enough?