Hi all
I am running VQSR for exome data and as a result of its first step i.e recalibration and calculation of VQSLOD, it also gives a tranche file which contains Ti/Tv ratios as one of the parameters along with others.
As per my knowledge the Ti/Tv ratio should be around 2.3 for exome data and it should decrease as the tranche size increases (from 90 to 99.-100). But in my case the trend of this ratio is reverse for novel variants (its fine for known variants) and is as follows:
targetTruthSensitivity numKnown numNovel knownTiTv novelTiTv minVQSLod filterName accessibleTruthSites callsAtTruthSites truthSensitivity
90 82669 3570 2.3897 0.9188 5.703 TruthSensitivityTranche0.00to90.00 39003 35102 0.9
99 95796 4084 2.3625 1.0044 2.3102 TruthSensitivityTranche90.00to99.00 39003 38612 0.99
99.9 106287 6236 2.3037 1.0132 -4.2613 TruthSensitivityTranche99.00to99.90 39003 38963 0.999
100 111724 9022 2.2558 1.1301 -37928.8734 TruthSensitivityTranche99.90to100.00 39003 39003 1
Is this a worry or it is supposed to be so. If yes then why?
Thanks in advance.
I am running VQSR for exome data and as a result of its first step i.e recalibration and calculation of VQSLOD, it also gives a tranche file which contains Ti/Tv ratios as one of the parameters along with others.
As per my knowledge the Ti/Tv ratio should be around 2.3 for exome data and it should decrease as the tranche size increases (from 90 to 99.-100). But in my case the trend of this ratio is reverse for novel variants (its fine for known variants) and is as follows:
targetTruthSensitivity numKnown numNovel knownTiTv novelTiTv minVQSLod filterName accessibleTruthSites callsAtTruthSites truthSensitivity
90 82669 3570 2.3897 0.9188 5.703 TruthSensitivityTranche0.00to90.00 39003 35102 0.9
99 95796 4084 2.3625 1.0044 2.3102 TruthSensitivityTranche90.00to99.00 39003 38612 0.99
99.9 106287 6236 2.3037 1.0132 -4.2613 TruthSensitivityTranche99.00to99.90 39003 38963 0.999
100 111724 9022 2.2558 1.1301 -37928.8734 TruthSensitivityTranche99.90to100.00 39003 39003 1
Is this a worry or it is supposed to be so. If yes then why?
Thanks in advance.
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