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How to run GATK directly on SRA files

Hello , I recently saw a webinar by NCBI "Advanced Workshop on SRA and dbGaP Data Analysis" ( They mentioned that they were able to run GATK directly on SRA files.

I downloaded GenomeAnalysisTK-3.5 jar file to my computer. I tried both these commands:

java -jar /path/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T HaplotypeCaller -R SRRFileName -I SRRFileName -stand_call_conf 30 -stand_emit_conf 10 -o SRRFileName.vcf

java -jar /path/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T SRRFileName -R SRR1718738 -I SRRFileName -stand_call_conf 30 -stand_emit_conf 10 -o SRRFileName.vcf

For both these commands, I got this error:
ERROR MESSAGE: Invalid command line: The GATK reads argument (-I, --input_file) supports only BAM/CRAM files with the .bam/.cram extension and lists of BAM/CRAM files with the .list extension, but the file SRR1718738 has neither extension. Please ensure that your BAM/CRAM file or list of BAM/CRAM files is in the correct format, update the extension, and try again.

I don't see any documentation here about this, so wanted to check with you or anyone else has had any experience with this.


Best Answers


  • Thank you for the prompt response.

  • Ben_BusbyBen_Busby NCBIMember

    Right now it works well if you launch the 'vdb' AMI in AWS.

  • Hello, I'd like to check if SRA support was added to GATK 3.6 or not.

    @Ben_Busby : We are trying to do this on our local machine , not on the cloud, so cannot use your AMI. Thanks.

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