Question: GATK BaseRecalibration - Error: Index not found
0
gravatar for deepue
4.3 years ago by
deepue110
Finland
deepue110 wrote:

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. 

baserecalibration snp gatk • 2.0k views
ADD COMMENTlink modified 4.3 years ago by RamRS23k • written 4.3 years ago by deepue110
1
gravatar for RamRS
4.3 years ago by
RamRS23k
Houston, TX
RamRS23k wrote:

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.

ADD COMMENTlink written 4.3 years ago by RamRS23k
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