I am trying to use Galaxy tools to create gVCF file to be used for building gd_SNP file format. The output files from FreeBayes are VCF. This can be done using Haplotypecaller of gatk which is not available in Galaxy. Is there any way to do this in Galaxy?
The GATK tools at http://usegalaxy.org are older (v 1.4) and are deprecated. Requests to expand the newer versions of GATK in the Tool Shed should be made directly to the tool authors.
That said, you do not need a gVCF file if using the Genome Diversity tools. If this is your goal, the tool Genome Diversity: Convert with the Freebayes VCF dataset as input. Make File is also an option to create gd_snp output, but since you already have a VCF, use that.
Best, Jen, Galaxy team