GATK BaseRecalibration - Error: Index not found
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9.1 years ago
deepue ▴ 160

Hi,

While using the BaseRecalibration step, I have got the below error message. I have already built index file for the reference hg19.

MESSAGE: An index is required, but none found., for input source: dbsnp_138.hg19.vcf.gz

Could you please help me in understanding the issue.

SNP GATK BaseRecalibration • 4.4k views
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1
Entering edit mode
9.1 years ago
Ram 44k

From your statement, it looks like you have indexed the hg19 reference sequence. You might need to index the VCF file as well. Use

tabix -p vcf dbsnp_138.hg19.vcf.gz

to index the VCF file.

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