Error in GATK haplotypecaller running

A USER ERROR has occurred: Fasta dict file file:///scratch/user/azharjameel/Pheasant_GBS_Part-1/ref/ncbi-genomes-2022-05-19/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.dict for reference file:///scratch/user/azharjameel/Pheasant_GBS_Part-1/ref/ncbi-genomes-2022-05-19/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b_genomic.fna 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.

I have all formate of files in the reference directory including genome.dict but still not running show the error, Please resolve the issues.

gatk

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updated 4.2 years ago by Ram

• written 4.2 years ago by Azhar Jameel •

what is this tag "hannah" ?

did you read https://gatk.broadinstitute.org/hc/en-us/articles/360035531652-FASTA-Reference-genome-format

Most GATK tools additionally require that the main FASTA file be accompanied by a dictionary file ending in .dict and an index file ending in .fai, because it allows efficient random access to the reference bases.

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written 4.2 years ago by Pierre Lindenbaum

I've changed that tag to GATK. It probably was a language barrier thing.

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written 4.2 years ago by Ram

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