20160412 - Workflow Priorities
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AboutThis document lets us track what workflows are in production, which are being worked on, and which have been requested. Add your requests to the list at the bottom. Identifying a "Docker Developer" is absolutely key on making progress with this. Contact Brian O'Connor <briandoconnor@ucsc.edu> and Melissa Cline <cline@soe.ucsc.edu> when adding.
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Current Production Workflows
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NameUsed By Exp DesignAuthorType
Release Version
DateDockerized?on Dockstore?Notes
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RNASeq-CGLRNASeqJohn V.RNASeq1.1YN
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RNASeq-UNC*RNASeqJohn V.RNASeq1.1NN
* this will likely be deprecated soon
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AlignmentWES/WGS - GermlineJohn V. Frank N.WES/WGS1.1NN
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ExomeVarJohn V.WES1.1NN
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In Progress Workflows/Tools
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NameUsed By Exp DesignAuthorType
Release Version
Date ETA for 1st release
Dockerized?on Dockstore?
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GATK Pre-processing PipelineWES/WGS - GermlineAudrey M.WES/WGSQ2NN
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Adam GATKWES/WGS - Germline
Frank N. Audrey M.
WES/WGSQ3NN
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AdamWES/WGS - Germline
Frank N. Audrey M.
Bam utilsQ3NN
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Germline GATKWES/WGS - Germline
Jacob P. Audrey M.
WES/WGSQ3NN
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ProtectImmunoArjun RaoImmunobetaQ3NN
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SpladderRNASeqJohn V.RNASeq alt splicingQ2??????
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JuncBaseRNASeqBrooks LabRNASeq alt splicing?????????
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PCAWG SomaticWGS - Somatic
Brian O. (Sanger, DKFZ/EMBL, Broad)
WGS SomaticQ3YY (3 out of 7)
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vg (genome graph)???Charles MarkelloWES/WGS GermlineQ3NN
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marginAlign (nanopore) ???
Art Rand/Miten Jain
WES/WGS GermlineQ3NN
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Requested (Tools or Full Workflows)
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NameDocker Developer
Original Author
Exp Design
Dockerized?
Dockstore?RequestorProjectDate NeededPriorityInput DataNotes
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Oncotator (or equivalent variant annotation), SnpEff/SnpSIFT (Jacob will do these, see ICGC portal), TrasVar, Angie H. with VAI?
Arjun->Jacob, Angie H., Jing?, Rachele
BroadWES/WGS - Germline/SomaticNN1
WES, infers how variant affects gene expression (e.g. synonymous, non-syn, non-coding, splice-site, stop codon, etc)
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SIFT, Polyphen2, MutationAssessor, OncoDrive-FM, VEST/CHASM (any/all of these), Muppet
see above, Jing?, RacheleWES/WGS - Germline/SomaticNN1WES, Infers impact of mutations
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exon-level quantification
John, but not an active area of work, Jacob said he could add this
UNCNN
Olena Morozova
CKCCASAP1RNASeq
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WES/WGS Alignment QCJacob & Olena & HollyWES/WGS - Germline/SomaticNNJosh StuartCKCC, WCDT1WES, quantifies read coverage across genome, strand bias, etc
Jeltje will look into this and ask Josh
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RNASeq downstream analysis preprocessing, followed by TumorMap
Yulia Newton & cross check with John
Yulia NewtonNN1
RNASeq - log transform, de-duplicating the names... talk to Sean Upchurch at CalTech to discuss RNA expression reporting... important for submission to standard DBs
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Genome Data Commons (GDC) workflows from U. ChicagoBrian O'ConnorU. Chicago
WES/WGS - Germline/Somatic, RNASeq
NN1all types
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3 or more variant callers across our pipelinesArjun, John, MC3, etc1
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Downstream annotation from various "tracks"... work on getting Foundation VCFs
Holly, Olena, and Max1
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Paradigm (closed source version, calling web service?)Chris WongCharlie VaskeWES/RNASeq???NNJosh Stuart
CKCC, WCDT, PanCanAtlas
Issues: 4RSEM gene-level RNASeq, GISTIC2, infers gene activity from pathway context
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OncoDriveFM
Max since he knows status (per David)
Nuria Lopez-Bigas, UPF
WES/WGS - Germline/SomaticNNJosh StuartCKCC, PanCanAtlas4WES, Infers impact of mutations
Talk to Max about this since he's worked with Nuria, databases for mutations that are already annotated so it's a simple lookup, really would be great to use these annotation tracks from browser
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ABSOLUTE???
Scott Carter, Broad
NN3WES, infers ploidy and cancer cell fraction
Won't do because requires manual choices
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PhyloWGS???Quaid MorrisWGS - SomaticNN5WES, CNA, infers heterogeneity and lineage reconstruction
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deFuseJeltje van Baren, Jacob Pfeil
Andrew McPherson
RNASeqNN
Olena Morozova
CKCCASAP4RNASeq, 38G of helper files
Jacob solved this problem
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RNASeqQC??NN1RNASeq
Done by John in 2.1 RNASeq-CGL pipeline
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GISTIC2
Now obsolete? Jeltje van Baren
WGS - SomaticNNJosh Stuart
CKCC, WCDT, PanCanAtlas
2WES, Infers gene-quantified copy number alterations
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Outlier analysisOlena Morozova & MedbookOlena MorozovaNN3RNASeq
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RSEMDeweyNN2RNASeq, Gene-level quantification
Done by John
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limma, SamSeq, DESeq2 (any/all of these)
Wolfgang Huber (DESeq2)
RNASeqNN3
RNASeq identifies differentially expressed genes given groupings of patient samples (e.g. agressive vs less aggressive)
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Viper-UnsupervisedAlana Weinstein?Evan PaullRNASeq - pathway enrichmentYN3
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TieDieAlana Weinstein?Evan PaullRNASeq - tumor subtypesNN3
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Xena Data HubJing ZhuBrian CraftNNJing Zhu4
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Machete, Prada, Kalisto (future support), etc to compare to DeFuse
Jacob to compare these tools
RNASeq - Gene Fusion
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Picard Collect RNASeq Metrics
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BamToFastqNHolly BealeCKCC
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FusionNHolly BealeCKCC
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RNA-Seq Variant CallingRNA-Seq Variant CallingNHolly BealeCKCCshould take FASTQ as input
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JuncBaseYNHolly BealeCKCC
derive from Docker that Max Haussler wrote
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CNV calling from tumor-normal exome dataNHolly BealeCKCC
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Workflows and Tools
QC Metrics and Tools