SNP Feature File Indexing
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!
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arjun.murthy779 •
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what version of GATK are you using? For v4.1.6.0 that parameter flag is
-Ihttps://gatk.broadinstitute.org/hc/en-us/articles/360041851771-IndexFeatureFile