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Comparative Analysis of GRCh37 and GRCh37B Using Schwartz Optical Maps and TPF/AGP

This report presents a comprehensive comparison between GRCh37 and GRCh37B, utilizing Schwartz Optical Maps and the TPF/AGP framework. Key areas of focus include the removal and addition of clones, gap coverage assessments, and the analysis of new clones related to whole genome sequencing. We evaluate variations in large regions of interest, pinpoint changes in anchor sequences, and examine the impact of these changes on alignment quality. The report highlights resolved issues, the significance of gap closures, and the general stability of alignment quality between the two versions.

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Comparative Analysis of GRCh37 and GRCh37B Using Schwartz Optical Maps and TPF/AGP

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Presentation Transcript

  1. Team Meeting

  2. Comparing GRCh37 with 37B • TPF/AGP • Schwartz Optical maps.

  3. TPF/AGP • Removed clones/seq • Added clones/seq • Gap coverage • New clones (wgs/gaps/contain?)

  4. GRCh37 TPF GRCh37B TPF Fetch Flanking Clone/Seq Gaps Fetch associated Region One or None Anchor Seq Both Flanking Anchor Seq Walk up to 8 GRCh37 TPF Places until GRCh37B hit Compare Region of Interest Large Region Change AGP

  5. Seq Added (Summary)

  6. OM Comparison • Schwartz 3-cell line Alignment. • Compare GRCh37 OM punchlists to see if resolved in GRCh37B.

  7. GRCh37 GRCh37B Fetch Punchlist Fetch Clone Region Extract Clone Region Fetch OM Frags Fetch Flanking Seq Compare OM Frags Between DB

  8. OM Comparison • FIXED REGIONS: 82 • of which are gaps related: 64 • of which have clone removed, but two flanking clones (500kb flank): 12

  9. Gap Closure (AC233715 –chr2)

  10. Chr6 centromere region (AL356131)

  11. Switchpoint resolution (AC073057)

  12. Removal of Clone (AP00662)

  13. Any thing in GRCh37B to make Alignment worse? • Apart from a clone swap, not really, introduction of small OM changes is not significant overall or compensated elsewhere.

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