SNP Feature File Indexing
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4.0 years ago

Hi! I am trying to index a SNP vcf file so that I can run a base recalibration on it. I have generated a first round filtered variant file, which I am indexing and using to run the Base recalibration.

The code I am using for this is: gatk IndexFeatureFile -F ref_1_filteredSNP.vcf

It is throwing me an error, saying that -F is not a recognized option.

Any advice on how to move furher would be greatly appreciated!

SNP genome bacterial • 1.3k views
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what version of GATK are you using? For v4.1.6.0 that parameter flag is -I https://gatk.broadinstitute.org/hc/en-us/articles/360041851771-IndexFeatureFile

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