ts_filter_level vs. tranche settings
Posted in Ask the GATK team | Last updated on 2012-11-12 19:53:09


Comments (5)

Hi,

I'm having a little trouble understanding the relationship between the -ts_filter_level and -tranche settings for VQSR. If I'm not mistaken the defaults are 99 and [100,99.9,99.0,90] respectively. When I run VQSR with these defaults, my tranches are altered because of the 99 ts filter level. I get:

##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=TruthSensitivityTranche99.00to99.90,Description="Truth sensitivity tranche level at VSQ Lod: -0.1838 <= x < 3.1102">
##FILTER=<ID=TruthSensitivityTranche99.90to100.00+,Description="Truth sensitivity tranche level at VQS Lod < -6135.0237">
##FILTER=<ID=TruthSensitivityTranche99.90to100.00,Description="Truth sensitivity tranche level at VSQ Lod: -6135.0237 <= x < -0.1838">

Is it odd that there are two tranches with the same ts values and different VQSLOD values? If I adjust the ts filter level to 90, I get what I originally expected to see:

##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=TruthSensitivityTranche90.00to99.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.5901 <= x < 4.8133">
##FILTER=<ID=TruthSensitivityTranche99.00to99.90,Description="Truth sensitivity tranche level at VSQ Lod: -0.692 <= x < 2.5901">
##FILTER=<ID=TruthSensitivityTranche99.90to100.00+,Description="Truth sensitivity tranche level at VQS Lod < -6.11002079587E7">

Is it just me, or does this seem to be an incompatibility between the defaults values? Which is more important, correct ts filtering or correct tranche intervals? We will at times filter based on these tranches, so I'd like to be setting them correctly. Thanks.

Ben


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