I have a number of vcfs that I need to index (create .idx files), which I attempted to do with GATK, e.g.
java -Xmx5g -jar $gatk_path/GenomeAnalysisTK.jar -T IndexFeatureFile -F N03_INDELS.vcf
Which returns an invalid argument error even though the vcf file is, as far as I can tell, in standard format.
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: IndexFeatureFile
I haven't used IndexFeatureFile before (usually the idx is automatically generated when I create vcfs from my alignments using GATK), so it isn't clear to me what's going wrong.