gatk-3.8/testdata/tranches.6.txt

# Variant quality score tranches file
# Version number 2
FDRtranche,targetTiTv,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName
0.10,2.80,15839,897,3.3052,2.8008,-3.8485,FDRtranche0.00to0.10
1.00,2.80,15844,900,3.3043,2.7815,-3.8652,FDRtranche0.10to1.00
2.00,2.80,15847,902,3.3051,2.7583,-3.8826,FDRtranche1.00to2.00
10.00,2.80,16153,1039,3.2744,2.5704,-5.1058,FDRtranche2.00to10.00
VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4684 348d0f76-0448-11de-a6fe-93d51630548a 2010-11-16 06:19:22 +08:00			`# Variant quality score tranches file`
			`# Version number 2`
			`FDRtranche,targetTiTv,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName`
			`0.10,2.80,15839,897,3.3052,2.8008,-3.8485,FDRtranche0.00to0.10`
			`1.00,2.80,15844,900,3.3043,2.7815,-3.8652,FDRtranche0.10to1.00`
			`2.00,2.80,15847,902,3.3051,2.7583,-3.8826,FDRtranche1.00to2.00`
			`10.00,2.80,16153,1039,3.2744,2.5704,-5.1058,FDRtranche2.00to10.00`