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Created 2013-10-02 00:56:39 | Updated | Tags: variantrecalibrator haplotypecaller queue mode

Comments (4)

Hi team, I have a basic question, sorry. I am trying to use HaplotypeCaller and VariantRecalibrator with QUEUE but I don't know how add:

VariantRecalibrator.mode = BOTH

HaplotypeCaller.genotyping_mode = DISCOVERY

I get a "not found: value BOTH/DISCOVERY" error.

Thank you in advance,

Created 2013-08-13 04:31:16 | Updated | Tags: variantrecalibrator indels snps mode

Comments (3)

For exome-sequencing, I was wondering how I should decide the "-mode" parameter? should I use "SNP" or "Indel" or both? I want to get both information in the final results, should I use "BOTH" -mode?