1 / 10

SeqWare Pipeline Status & HOWTO May 4, 2010: Nelson Lab Meeting Jordan Mendler Nelson Lab, UCLA Human Genetics Depar

SeqWare Pipeline Status & HOWTO May 4, 2010: Nelson Lab Meeting Jordan Mendler Nelson Lab, UCLA Human Genetics Department jmendler@ucla.edu. Status. 0.6.2.2 is latest 'stable' release Alignment with Bfast Variant Calling with SamTools/Pileup VariantDB Creation with BerkeleyDB

gallagher
Download Presentation

SeqWare Pipeline Status & HOWTO May 4, 2010: Nelson Lab Meeting Jordan Mendler Nelson Lab, UCLA Human Genetics Depar

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. SeqWare Pipeline Status & HOWTO May 4, 2010: Nelson Lab Meeting Jordan Mendler Nelson Lab, UCLA Human Genetics Department jmendler@ucla.edu

  2. Status • 0.6.2.2 is latest 'stable' release • Alignment with Bfast • Variant Calling with SamTools/Pileup • VariantDB Creation with BerkeleyDB • 0.7.0 is in development (SVN Trunk) • Alignment with ??? • Separate MarkDuplicate workflow • Variant Calling Picard/Pileup • VariantDB Creation with BerkeleyDB & HBase??

  3. Pipeline 0.6.2.2 • Updates from 0.6.2.1 • Fixed permission denied bug from /share/apps • Authentication is automatic (grid-proxy-init) • Importing is automatic (bin/pegasus-rc-import.sh) • Setup of pegasus-config directory is automatic • Demo will follow • First time: setup credentials • Can be autogenerated by SysAdmin for all users • Every other time: simply a bin/pegasus-run.sh

  4. Pipeline 0.7.0 (Development) • Updates from 0.6.x • Metadata writeback works • Tracks stdout, stderr, status, etc while processing • Stores dependency of jobs and 'task groups' • Bfast → Merge → Pileup • localalign 1 → postprocess 1 … → pileup chr 1 • Bfast Localalign → localalign 1, localalign2, localalign3, ... • Conforms to MetataDB schema for LIMS integration • Variant Calling uses Picard for merge, sort, etc • Merging/MarkDuplicate is a separate workflow • Different libraries within a single experiment • Force consistent/intuitive directory structure and naming

  5. Pipeline 0.7.0: Status • Awaiting 0.7.0 Schema freeze for minor adjustments • As point of convergance, Schema will stay fixed until 1.0 • In progress • MarkDuplicates workflow • Kevin started using the Python API • 2-3 'days' of work left • LIMS • Waiting for Brian's status update on Wednesday • Command Line Interface • Bret/Kevin? • Finished • Metadata writeback works • Force consistent/intuitive directory structure and naming • Port to Picard

  6. Pipeline 0.8+ • Post 0.7.0 Features: • Move to Python/Perl API for workflows • Much faster turn around time • Support new methods • Alignments to use ?? • VariantDB to use HBase • Automation for end-users • Workflow to move data from sequencers (Jordan) • Previously awaiting Pegasus PM-131 (fixed upstream 5/3/2010) • LIMS (Brian) • Command Line Interface (Bret/Kevin) • Agent to run workflows scheduled by LIMS/CLI (Jordan) • Awaiting schema freeze

  7. Alignment

  8. VariantDB

  9. SeqWare Pipeline: Demo • Wiki is up-to-date as of May 3, 2010 • Nelsonlab for Users • Sequence_Analysis_Workflow_HOWTO • https://secure.genome.ucla.edu/index.php/Sequence_Analysis_Workflow_HOWTO • Sourceforge for Developers • http://seqware.sf.net • Both for Admins • SeqWare: http://seqware.sf.net • Pegasus: https://secure.genome.ucla.edu/index.php/Pegasus • Consolidation into 1 wiki in the future • Demo follows Sequence_Analysis_Workflow_HOWTO

More Related