HaplotypeCaller does not recognize the RefSeqfile

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Newcomer

• March 18, 2020 09:18

Hi! I am using GATKver4.1.4.1. I am running this.

gatk --java-options "-Xmx4g" HaplotypeCaller -R Bos_taurus.ARS-UCD1.2.dna.toplevel.fasta -I maeked_SRR6942513_addRG.bam -O output_SRR6942513.vcf.gz -ERC GVCF

I geted error

A USER ERROR has occurred: Fasta index file file:///home/oomori/ncbi/public/sra/Bos_taurus.ARS-UCD1.2.dna.toplevel.fasta.fai for reference file:///home/oomori/ncbi/public/sra/Bos_taurus.ARS-UCD1.2.dna.toplevel.fasta 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.

But i maded dict file and .fai file

Bos_taurus.ARS-UCD1.2.dna.toplevel.fa.dict
Bos_taurus.ARS-UCD1.2.dna.toplevel.fa.fai

why doesn't recognized fasta file ?

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• 

  Bhanu Gandham

  • March 18, 2020 22:40

  Hi Newcomer

   

  Your input fasta file is Bos_taurus.ARS-UCD1.2.dna.toplevel.fasta. GATK is looking for Bos_taurus.ARS-UCD1.2.dna.toplevel.fasta.fai and not Bos_taurus.ARS-UCD1.2.dna.toplevel.fa.fai. Take a look at the suffixes. Once you fix that it should be good to go.

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  Newcomer

  • March 23, 2020 05:10

  Thanks!

  When I fixed f.dict and .fai file , it worked fine.

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