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Stringent breakpoints

Stringent breakpoints. Alexej & Ken, August 17, 2011. Stringent requirements for b -points. More stringent requirements for AGE alignment (remove ~8% of b -points) I ncrease stringency on contigs used by both AGE and Crossmatch (strong effect on the number of resulting breakpoints ).

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Stringent breakpoints

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  1. Stringent breakpoints Alexej & Ken, August 17, 2011

  2. Stringent requirements for b-points • More stringent requirements for AGE alignment (remove ~8% of b-points) • Increase stringency on contigs used by both AGE and Crossmatch(strong effect on the number of resulting breakpoints)

  3. Phase1 deletion breakpoint assembly First line – initial b-points Second line – stringent b-points Much better agreement between AGE and CROSSMATCH

  4. First line – initial b-points Second line – stringent b-points All calls from 5 merged calls Inconsistent FDR estimation: (2108 – 519)/2108 = 75% < 86%

  5. Calls with SAV p-val <> 0.5 Require 50% reciprocal overlap Second line – p-val > 0.5 • Calls with p-val < 0.5 and p-val > 0.5 are not dramatically different • SAV validation seems to systematically overestimate FDR. • Possible reasons: • Input call properties (sample under-assignment) • Bias again smaller regions • Bias in repetitive regions • Reference sample bias when using aCGH probes

  6. Proposal • Use GenomeStrip + assembly support (all or only with both AGE and CROSSMATCH support) + SAV validated (possibly) • SAV validation has inherent biases • Assembly validation is orthogonal to SAV validation • There is evidence that SAV overestimates FDR • GenomeStrip + assembly support by both AGE and CROSSMATCH would have 29,281 calls with likely overestimated SAV FDR of 11% • Use only consistent b-points by AGE and CROSSMATCH for genotyping

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