Can someone please assist me with the following. I am new to GATK(3.8), and I want to run the RealignerTargetCreator command according to what is specified on the GATK website.
This is my specific command:
>singularity exec /tools/containers/gatk/gatk-3.8--py36_4.simg java -jar GenomeAnalysisTK.jar \ -T RealignerTargetCreator \ -R ~/Analysis_data/GATK/refs/ref.fa \ -known ~/Analysis_data/GATK/Mills_and_1000G_gold_standard.indels.hg38.vcf \ -known ~/Analysis_data/GATK/Homo_sapiens_assembly38.known_indels.vcf \ -I marked_dup.bam \ -o forIndelRealigner.intervals
but I get the following error message:
> ERROR MESSAGE: Fasta index file /usr/people/sfernol/Analysis_data/GATK/refs/ref.fasta.fai.fai for reference /usr/people/sfernol/Analysis_data/GATK/refs/ref.fasta.fai does not exist.
I read up on similar problems and I tried putting the different reference files in the same location, but i still get the same error.
I used Picard for creating the .dict file and samtools for indexing my reference genome file, so i have those two files and the original fasta file in the same folder.
I am not sure what I am doing wrong, please help?