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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
-an DP -an QD -an FS -an HaplotypeScore -an MQRankSum -an
ReadPosRankSum -an InbreedingCoeff -mode INDEL -recalFile