I want to convert .ht2 files into FASTA file. as I have obtained .ht2 files from Hisat2 tool and now I need to convert these files into fasta format please help? these .hts2 files are obtained as I have indexed my reference genome. now, I am calling haplotypecaller from GATK tools for haplotypes and it needs INDEXED reference genome as I have .hts2 index files.GATK is not accepting those files as it only accepts fasta file. please guide me?
P.S- after running hisat2, there are 8 resulting files.