Hi, i am using the GATK version gatk/4.2.2.0 for HaplotypeCaller. I have been facing the reference.fa indexing issue. I tried to index the file using the following command

samtools faidx ~/path/PitayaGenomic.fa

#three difference formats of reference files 
-rw-r--r-- 1 tariqr 1.3G Feb 21 17:50 PitayaGenomic.fa
-rw-r--r-- 1 tariqr  34K Feb 21 20:01 PitayaGenomic.fa.fai
-rw-r--r-- 1 tariqr 137K Feb 21 21:05 ref.dict

I tried to use all three formats in GATK but facing the following errors. The first error using the .fai format

java.lang.IllegalArgumentException: File is not a supported reference file type: ~/path/genome_gatk/PitayaGenomic.fa.fai

Second error using .fa file

A USER ERROR has occurred: Fasta dict file file:///path/genome_gatk/PitayaGenomic.dict for reference file:///path/genome_gatk/PitayaGenomic.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.

Third error after using the ref.dict format

java.lang.IllegalArgumentException: File is not a supported reference file type: ~/path/genome_gatk/ref.dict

Please suggest to me what should I do to fix the issue of reference. I really acknowledge your kind suggestion. The code is given here:

gatk HaplotypeCaller -R ~/path/genome_gatk/PitayaGenomic.fa -I ~/path/input.bam -O ~/path/output.g.vcf.gz --bam-output ~/path/output.bam -ERC GVCF --native-pair-hmm-threads 8