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Mauricio Carneiro 9f74969e3a BQSR with GATKReport implementation 
* restructured BQSR to report recalibrated tables.
   * implemented empirical quality calculation to the BQSR stage (instead of on-the-fly recalibration)
   * linked quality score quantization to the BQSR stage, outputting a quantization histogram
   * included the arguments used in BQSR to the GATK Report
   * included all three tables (RG, QUAL and COVARIATES) to the GATK Report with empirical qualities

On-the-fly recalibration with GATK Report

   * loads all tables from the GATKReport using existing infrastructure (with minor updates)
   * implemented initialiazation of the covariates using BQSR's argument list
   * reduced memory usage significantly by loading only the empirical quality and estimated quality reported for each bit set key
   * applied quality quantization to the base recalibration
   * excluded low quality bases from on-the-fly recalibration for mismatches, insertions or deletions
 		2012-03-23 15:42:32 -04:00
..
vcf Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
HiSeq.10000.bgzip.vcf.gz Adding bgzip vcf file for unit tests 2011-09-21 15:39:45 -04:00
HiSeq.10000.vcf Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
HiSeq.10000.vcf.gz GZIP VCF for testing 2011-08-19 09:05:39 -04:00
TabularDataTest.dat Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
TabularDataTest2.dat Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ValidatingPileupTargets.list Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
breakpoint-example.vcf Added support for breakpoint alleles 2012-02-23 12:14:48 -05:00
ceutrio.ped Oops, forgot the PED test file 2011-10-05 21:09:08 -07:00
defaultGATKConfig.cfg Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
diffTestMaster.vcf First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure. 2011-07-04 16:11:42 -04:00
diffTestTest.vcf First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure. 2011-07-04 16:11:42 -04:00
exampleBAM.bam PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleBAM.bam.bai PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleBAM.simple.bai Testdata for diffObjects. 2011-07-18 10:47:03 -04:00
exampleBAM.simple.bam Testdata for diffObjects. 2011-07-18 10:47:03 -04:00
exampleDBSNP.vcf PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleFASTA.dict Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exampleFASTA.fasta Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exampleFASTA.fasta.amb Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.ann Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.bwt Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.fai Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exampleFASTA.fasta.pac Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rbwt Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rpac Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rsa Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.sa Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleNORG.bam Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
exampleNORG.bam.bai Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
gFFTest.gff Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
gatkrunreport.fail.xml analyzeRunReports cleanup for new minimal GATKRunReport structure 2012-03-12 09:46:26 -04:00
gatkrunreport.success.xml analyzeRunReports cleanup for new minimal GATKRunReport structure 2012-03-12 09:46:26 -04:00
genotypes_chr1_ASW_phase3.3_first500.hapmap Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
logisticParamsTest.list Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
overlapTest.bed Testdata for IntervalStratification 2011-11-10 11:08:34 -05:00
recalConfig_1KG.cfg Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
sampleBedFile.bed Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
small.dbsnp.rod Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
tranches.4.txt Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
tranches.6.txt Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
tranches.raw.dat Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
withSymbolic.b37.vcf Testdata for IntervalStratification 2011-11-10 11:08:34 -05:00