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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

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

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  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

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