Comparing GRCh37 with 37B • TPF/AGP • Schwartz Optical maps.
TPF/AGP • Removed clones/seq • Added clones/seq • Gap coverage • New clones (wgs/gaps/contain?)
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
OM Comparison • Schwartz 3-cell line Alignment. • Compare GRCh37 OM punchlists to see if resolved in GRCh37B.
GRCh37 GRCh37B Fetch Punchlist Fetch Clone Region Extract Clone Region Fetch OM Frags Fetch Flanking Seq Compare OM Frags Between DB
OM Comparison • FIXED REGIONS: 82 • of which are gaps related: 64 • of which have clone removed, but two flanking clones (500kb flank): 12
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.