Good day
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?
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written
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granecious •
samtools faidx ~/Analysis_data/GATK/refs/ref.fa
We use the faidx command in samtools to prepare the fasta index file. This file describes byte offsets in the fasta file for each contig, allowing us to compute exactly where a particular reference base at contig:pos is in the fasta file.
Hi
I managed to solve my problem. I had to rename my sam indexed file to correspond to my ref.fa, since my file formats were different GATK could not pick up my index file.
I renamed my index file from ref.fasta.fai to ref.fa.fai and it worked.
We had same error. When we re-create the dict file with no ".fa.dict" suffix, but only ".dcit" suffix, it work correctly.
we have the same error; The specified fasta file doesn't exist, renamed according to the given suggestion above, and run multiple times still the same issue. is there any suggestion please. thanks
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