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Question related to VQSR

MUHAMMADSOHAILRAZAMUHAMMADSOHAILRAZA Beijing Institute of Genomics, CASMember

Hi Everyone,
It might be very basic but I just want to reach some clarifications what i understand after applying VQSR steps to WGS sequencing data.

For SNPs
I've set tranches as described in the best practice document, i.e. -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 during "VariantRecalibrator" step and set "--ts_filter_level 99.5" in "ApplyRecalibration" step. All the SNPs annotated into "VQSRTrancheSNP99.90to100.00" and PASS Flags.
My question is should i filtered out all the SNPs marked with "VQSRTrancheSNP99.90to100.00" tranche. But when i looked "SNP variant Tranche plot", there are some tranche-specific true positive (TP) SNPs of 99.90 and 100.0 tanches as well. How you explain this according to GATK recommendations??

For INDELs case
I've set tranches as described in the best practice document, i.e. -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 during "VariantRecalibrator" step and set "--ts_filter_level 99.0" in "ApplyRecalibration" step. All the SNPs annotated into "VQSRTrancheSNP99.00to99.90", "VQSRTrancheSNP99.90to100.00" and PASS Flags. Becaise INDEL's VQSR transche plot was not generated so i have no idea of true and false positive percentage of INDELs.

Do you have any recommendations? In short should we filtered out all the VQSR marked variants and retain the rest (i.e. PASS) inside call set??

Thank you very much!

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