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Using IndexFeatureFile to index vcf

I have a number of vcfs that I need to index (create .idx files), which I attempted to do with GATK, e.g.

java -Xmx5g -jar $gatk_path/GenomeAnalysisTK.jar -T IndexFeatureFile -F N03_INDELS.vcf

Which returns an invalid argument error even though the vcf file is, as far as I can tell, in standard format.

##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find    walker with name: IndexFeatureFile

I haven't used IndexFeatureFile before (usually the idx is automatically generated when I create vcfs from my alignments using GATK), so it isn't clear to me what's going wrong.

gatk
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written by shpak.max • shpak.max

1 answer

there no such tool in gatk3.8

 java -jar gatk-3.8/GenomeAnalysisTK.jar -h 2>&1 | grep Index

it looks like it exists in gatk4.* https://gatk.broadinstitute.org/hc/en-us/articles/360037428111-IndexFeatureFile

anyways, it's more 'standard' to work with '*.vcf.gz" files indexed with bcftools index -t -f in.vcf.gz

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks. Is there anything analogous in GATK 3 that would create idx files?

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written by shpak.max • shpak.max

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