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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
/home/hufeng/Research/WESEBV/Data/VCF/CAEBV1raw.vcf
-resource:hapmap,known=false,training=true,truth=true,prior=15.0
/home/hufeng/Research/WESEBV/b37/hapmap_3.3.b37.sites.vcf
-resource:omni,known=false,training=true,truth=false,prior=12.0
/home/hufeng/Research/WESEBV/b37/1000G_omni2.5.b37.sites.vcf
-resource:goldstandindels,known=true,training=false,truth=false,prior=6.0
/home/hufeng/Research/WESEBV/b37/Mills_and_1000G_gold_standard.indels.b37.vcf
-an DP -an QD -an FS -an HaplotypeScore -an MQRankSum -an
ReadPosRankSum -an InbreedingCoeff -mode INDEL -recalFile
/home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelvcf.recal
-tranchesFile /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelvcf.tranches
-rscriptFile /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelrecal.plots.r

Answers

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