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This special page shows all uploaded files. When filtered by user, only files where that user uploaded the most recent version of the file are shown.

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descDate Name Thumbnail Size User Description Versions
13:41, 26 April 20123 23 12 whiteboard.jpg (file)1.86 MBDepristo 1
13:41, 26 April 20124 5 12 whiteboard.jpg (file)1.77 MBDepristo 1
15:58, 10 February 2012ThreadedIO.png (file)66 KBHanna 1
15:44, 30 January 2012SnpEff indels.pdf (file)238 KBDroazen 1
15:44, 30 January 2012SnpEff snps ensembl 64 vs 65.pdf (file)244 KBDroazen 1
15:43, 30 January 2012SnpEff snps comparison of available versions.pdf (file)360 KBDroazen 1
16:05, 11 January 2012Multiallelic.pptx (file)203 KBEbanks (Multi-allelic generalization of the Exact AF calculation.)1
16:04, 11 January 2012Multiallelic.pdf (file)84 KBEbanks (Multi-allelic generalization of the Exact AF calculation.)1
08:09, 19 December 2011Depristo cv.pdf (file)75 KBDepristo 4
18:16, 12 December 2011Pacbio processing pipeline.jpg (file)467 KBCarneiro 1
15:36, 25 October 2011FragmentPileupBenchmark.jpg (file)200 KBDepristo 1
10:08, 30 August 2011Samtools.pdf (file)398 KBEbanks 1
13:57, 3 August 2011Dinculeotide illumina.png (file)92 KBRpoplin (Residual error between reported and empirical quality scores as a function of dinucleotide context both before and after applying the GATK recalibration procedure for a lane sequenced at the Broad by an Illumina GA-II in February 2010.)1
13:56, 3 August 2011Machine cycle illumina.png (file)133 KBRpoplin (Residual error between reported and empirical quality scores as a function of machine cycle both before and after applying the GATK recalibration procedure for a lane sequenced at the Broad by an Illumina GA-II in February 2010.)1
13:55, 3 August 2011Distribution qual illumina.png (file)154 KBRpoplin (Distribution of reported quality scores both before and after applying the GATK recalibration procedure for a lane sequenced at the Broad by an Illumina GA-II in February 2010.)1
13:54, 3 August 2011Rep qual vs emp qual illumina.png (file)117 KBRpoplin (Reported quality score versus empirical quality score both before and after applying the GATK recalibration procedure for a lane sequenced at the Broad by an Illumina GA-II in February 2010.)1
13:51, 3 August 2011Rep qual vs emp qual illumina.pdf (file)83 KBRpoplin (Reported quality score versus empirical quality score both before and after applying the GATK recalibration procedure for a lane sequenced at the Broad by an Illumina GA-II in February 2010.)1
17:13, 13 May 2011Queue debug.png (file)143 KBKshakir 1
10:04, 6 May 2011Tranches.jpg (file)72 KBRpoplin 3
09:52, 6 May 2011Vqsr.tutorial.plots.R.HaplotypeScore.MQRankSum.png (file)355 KBRpoplin (VQSR model plot for wiki tutorial NA12878 HiSeq data set. The two dimensions show are mapping quality rank sum test as a function of haplotype score.)1
13:25, 2 May 2011Gatk development lifecycle.jpg (file)75 KBDepristo 1
11:29, 30 March 2011DataProcessingPPL.jpg (file)211 KBCarneiro (Data Processing Pipeline (the recommended best practices))1
10:39, 30 March 2011Fullcallingpipeline diagram.png (file)223 KBKiran (Diagram of the FullCallingPipeline)1
16:26, 22 March 2011PbGenotypeAndValidate.jpg (file)337 KBCarneiro (disambiguate between not confident calls and confident ref calls.)5
21:02, 14 March 2011Example.yaml (file)590 BCorin 2
18:08, 16 February 2011ExampleYaml.png (file)45 KBCorin (A screen shot of an example yaml file.)1
18:50, 14 January 2011Sting project libraries.png (file)97 KBKshakir 1
18:50, 14 January 2011Sting module sources.png (file)139 KBKshakir 1
18:50, 14 January 2011Sting module scala facet.png (file)126 KBKshakir 1
18:49, 14 January 2011Sting module dependencies.png (file)113 KBKshakir 1
16:48, 4 January 2011TiTv free VQSR.pdf (file)116 KBDepristo 1
16:47, 4 January 2011Tv-free variant quality score recalibration.pdf (file)116 KBDepristo 2
18:13, 16 December 2010GenomeStripSchematic.png (file)97 KBBhandsaker 1
18:09, 16 December 2010GenomeStripSchematic.jpg (file)117 KBBhandsaker 1
15:29, 10 December 2010BAQ in the gatk.pdf (file)991 KBDepristo 1
23:36, 8 December 2010StrandBias.png (file)50 KBEbanks 2
12:56, 30 November 2010Ngs tutorial depristo 1210.pdf (file)5.74 MBDepristo 1
15:05, 5 October 2010BWA read group patch.diff (file)18 KBDepristo 2
11:34, 29 September 2010Untitled.jpg (file)262 KBDepristo 1
11:25, 29 September 2010Best practice calls.jpg (file)447 KBDepristo 1
11:02, 29 September 2010Titv expectations.jpg (file)299 KBDepristo 1
13:32, 22 September 2010Overall flow.jpg (file)283 KBDepristo 1
10:24, 20 September 2010Developer overview.png (file)79 KBAaron 1
22:28, 19 September 2010HierarchicalParallelism.png (file)52 KBHanna 2
21:37, 8 September 2010ClusterPlot.QD vs SB.png (file)1.06 MBKiran (SNP clustering plot in two dimensions: QD (quality score / depth of coverage) vs. SB (strand bias).)1
20:03, 13 August 2010Queue attach sources.png (file)85 KBKshakir 2
20:02, 13 August 2010Scala dependencies.png (file)156 KBKshakir 2
15:39, 13 August 2010IndelRealignmentAlgorithm.png (file)95 KBEbanks 1
14:43, 10 August 2010Lib folder.png (file)115 KBKshakir 1
14:34, 9 August 2010QueuePipeline.jpg (file)82 KBKshakir 1

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