Apply GATK MuTect2 to SRA file


I am running GATK MuTect2 to two SRA files,

java -jar GenomeAnalysisTK.jar -T MuTect2 -R hg19.fa -I:tumor SRR537193.sra -I:normal SRR537200.sra -o SRR537193.output.vcf

but received this error:

ERROR MESSAGE: Cannot merge sequence dictionaries because sequence CM000672.1 and CM000668.1 are in different orders in two input sequence dictionaries.

It seems that these two SRA files have different chromosome order in the headers. Since they are whole-genome sequencing data, sam-dump is extremely slow. I wonder if there is better way to make this work without converting them to bam files.


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