I try some reference genome such as Homo_sapiens_assembly38.fasta and Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa but I still got the error below. Would you please have a suggestion? Thank you so much. The link in the error message doesn't work.
gatk BaseRecalibrator -I Library_1Aligned.out.sorted.bam -R /home/user/Homo_sapiens.GRCh38.dna_sm.primary_assembly .fa --known-sites 1000G_phase1.snps.high_confidence.hg38.vcf.gz --known-sites Homo_sapiens_assembly38.known_indels.vcf.gz -O recal_data.table A USER ERROR has occurred: Fasta dict file file:///oak/Homo_sapiens.GRCh38.dna_sm.primary_assembly.dict for reference file:///oak/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.