Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

VariantRecalibrator INDEL mode

Sorry for the naive question, it is my first time to use GATK and I am following
I am wondering if anyone has used the VariantRecalibrator from GATK to
recalibrate the SNPs and Indels, from the documentation I got to know
how to use that in SNP mode, but not still not sure how can I use that
in Indel mode. Do you know something about that?

And I have pasted my command below, not sure if I got that correct.
Thanks very much.

java -jar GATK/GenomeAnalysisTK.jar -T VariantRecalibrator -R
/home/hufeng/Research/WESEBV/b37/human_g1k_v37_decoy.fasta -input
-an DP -an QD -an FS -an HaplotypeScore -an MQRankSum -an
ReadPosRankSum -an InbreedingCoeff -mode INDEL -recalFile
-tranchesFile /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelvcf.tranches
-rscriptFile /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelrecal.plots.r


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