GATK showing error of reference file index

Question

[rj.rezwan]

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

[Medhat]

The command uses: -R ~/path/PitayaGenomic.fa
However, the error says: path/genome_gatk/PitayaGenomic.fa

I see in your command that there is no genome_gatk

[rj.rezwan]

I have modified the question. Please have a look and suggest the answer

[Ram]

They're not 3 different formats. .fai is the index of the .fa. .dict is a different format, sure.

Run this command and then try your GATK command:

cd ~/path/
ln -s ref.dict PitayaGenomic.dict

[rj.rezwan]

still same issue

java.lang.IllegalArgumentException: File is not a supported reference file type

[Ram]

I used ~/path/ which seems to be the wrong place. Can you show us the output to:

cd ~/path/genome_gatk/
ln -s ref.dict PitayaGenomic.dict
pwd
ls -l