I am also having a problem with HaplotypeCaller - when I set the flag to print out full haplotypes, no haplotype files are created. Here is my command:
java -jar /home/chodon/applications/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/chodon/comb_eny/abyss/final_contigs/A2/Assembly.fasta -I /home/chodon/comb_eny/abyss/final_contigs/A2/bowtie2_out/A2.sorted.bam --fullHaplotype --ignoreLaneInfo -o /home/chodon/comb_eny/abyss/final_contigs/A2/GATK_haplo2.out
Any help is much appreciated! Thanks, C