Embed Size (px)
DESCRIPTION
Slides on geval and 1KG by Laura Clarke
Citation preview
gVAL Browser and the GRC TrackHubLaura Clarke
http://geval.sanger.ac.uk/
• gVAL Browser
• GRC TrackHub
• 1000 Genomes and GRCh38
gEVAL Browser
• Evaluation of Genome Assemblies
• Based on Ensembl Framework
• Run by Sanger Institute
• Navigation of current assemblies
• View different annotation
• Punchlists of Assembly Issues
http://geval.sanger.ac.uk/
gEVAL Browser - Annotation
• Intra species alignments• Optical Map data• Clone End mapping• Black Tags/Clone sequence anomalies• Self Comparisons• CCDS Alignments• RefSeq Alignments• Repeat Annotation
– Centromeric repeats– Telomeric repeats– 1000 Genomes identified Mobile Element Insertions
http://geval.sanger.ac.uk/
Human Build Info
• Primary Reference
– GRCh38
• Current Build
– Human 20140826
• Older Versions
– GRCh37.p13
– NCBI36
• Other Assemblies
– CHM1_1.1
– NA12878
– Huref
– YH2.0
http://geval.sanger.ac.uk/
http://geval.sanger.ac.uk/
Intra-species comparisons
GRCh37 vs HuRef
HuRef
GRCh37
GRCh38
http://geval.sanger.ac.uk/
HuRef
GRCh38
http://geval.sanger.ac.uk/
GRCh37
GRCh38 fix.
HG-1312 (add wgs to PATH)
Add fix to GRCh38
http://geval.sanger.ac.uk/
Clone End Library Mappings
Mapped 1 time
Spanning partner in the vicinity
Wrong direction (<<, <>, >>)
Mapped multiple times
Wrong distance from partner
19 Human Clone Libraries• Reveals state of assembly
• Orientation• Mis-assemblies• Incorrect location
• Source of new sequence
http://geval.sanger.ac.uk/
Clone End Library Mappings
Clone End Library Mappings
http://geval.sanger.ac.uk/
Using Clone End Library Mappings
before
after
http://geval.sanger.ac.uk/
Optical Maps• ..ordered restriction maps from single stained molecules of
DNA.
• D.Schwartz (UW-Madison)
http://geval.sanger.ac.uk/
TrackHub
http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txtDisplay GRC issues in Ensembl and UCSC• Genome issues under review by the GRC• Genomic regions defined by the GRC• Alignments between the primary assembly and
alternate loci or patches• Clone sequence anomalies• Human regions with clones from the CHORI-17 library
(CHM1tert)
Adding a TrackHub to Ensembl
http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt
Adding a TrackHub to Ensembl
TrackHub Display 1:12956267-13431650
Adding a TrackHub to UCSC
Adding a TrackHub to UCSC
TrackHub Display 1:12956267-13431650
TrackHub Display 1:12956267-13431650
The 1000 Genomes Project
• IGSR established to maintain 1000 Genomes Data
• Phase 3 release is out on GRCh37
• Reads will be remapping in 1Q 2015
• dbSNP has GRCh38 mapping for most sites now
• Plan to recall/map in 2Q 2015
Acknowledgments
GRIT (Team135)• Kate Auger• Joanna Collins• Guy Griffith• Glenn Harden• Paul Heath• Britt Kilian• Kerstin Howe• Sarah Pelan• Glen Threadgold• James Torrance• Jo Wood
Alumni• Kim Brugger• Mario Caccamo• Ian Sealy• Tina Eyre• Ed Zuiderwijk
• James Smith• Paul Bevan
• Simon Brent• Harpreet Riat
• David Harper
• David Schwartz (UW Madison)• Steve Goldstein (UWMadison)
• Evan Eichler (Uwashington)• Jeff Kid (Uwashington)
http://geval.sanger.ac.uk/
