GATK BaseRecalibration - Error: Index not found

Question

[deepue]

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.

Answer 1

[Ram]

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.