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DP parameter VQSR for Targeted Exome Sequencing

AswathyNAswathyN BangaloreMember

Hello,
I perform variant calling on Targeted Exome Samples.
I read in a GATK forum that "-an DP" should not be used in VQSR step of Targeted Exome Sequencing samples.
http://gatkforums.broadinstitute.org/discussion/1259/which-training-sets-arguments-should-i-use-for-running-vqsr

I tried variant calling with DP and without DP parameters and could not make out any significant change.
Could you please confirm if DP should be used or not?

Thanking you in advance,
Aswathy

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