Bionano Solve Theory of Operation: Structural Variant Calling Document Number: 30110 Document Revision: J For Research Use Only. Not for use in diagnostic procedures. Copyright© 2020 Bionano Genomics, Inc. All Rights Reserved. For Research Use Only. Not for use in diagnostic procedures. Table of Contents Legal Notice ........................................................................................................................................... 4 Introduction ............................................................................................................................................ 5 Structural variant calling with Bionano Solve .......................................................................................... 5 De novo assembly .............................................................................................................................. 5 SV calling ........................................................................................................................................... 6 Zygosity classification ......................................................................................................................... 9 Confidence modeling .......................................................................................................................... 9 Copy number variant (CNV) calling ................................................................................................... 11 Introduction ..................................................................................................................................................... 11 Input ................................................................................................................................................................. 11 Output .............................................................................................................................................................. 12 Environment setup ........................................................................................................................................ 13 Usage .............................................................................................................................................................. 13 Theory ............................................................................................................................................................. 15 Masking ............................................................................................................................................ 33 SVMerge .......................................................................................................................................... 34 Rare Variant Pipeline (RVP) ............................................................................................................. 34 Structural variant calling performance: Rare Variant Pipeline............................................................... 36 Structural variant calling performance using simulated data ............................................................. 36 Summary ......................................................................................................................................................... 36 Performance for simulated insertions and deletions ................................................................................ 36 Performance for simulated duplications, translocation breakpoints, and inversion breakpoints ....... 37 Structural variant calling performance using real data....................................................................... 38 Structural variant calling performance: de novo assembly pipeline ...................................................... 39 Structural variant calling performance using simulated data ............................................................. 39 Performance for simulated insertions and deletions ................................................................................ 39 Performance for other simulated events .................................................................................................... 40 Structural variant calling performance using real data....................................................................... 40 Performance for insertions and deletions .................................................................................................. 40 Performance for translocation breakpoints2 .............................................................................................. 41 Performance for inversion breakpoints2 ..................................................................................................... 42 Copy number variant calling performance: fractional CN analysis ........................................................ 43 Copy number variant calling performance using simulated data ....................................................... 43 Copy number variant calling performance using real data ................................................................ 45 Copy number variant calling performance: integer CN analysis ........................................................... 46 Copy number variant calling performance using simulated data ....................................................... 46 Copy number variant calling performance using real data ................................................................ 47 Bionano Access integration ................................................................................................................. 48 VCF conversion ................................................................................................................................... 48 Additional Considerations .................................................................................................................... 48 30110 Rev J, Bionano Solve Theory of Operation: Structural Variant Calling Page 2 of 93 For Research Use Only. Not for use in diagnostic procedures. FAQs ................................................................................................................................................... 49 Appendix A: Performance for for simulated events .............................................................................. 54 RVP SV calling performance at lower coverage levels...................................................................... 54 Method for assessing SV calling performance .................................................................................. 56 SV calling performance with simulated data ............................................................................................. 56 SV calling performance with real data ........................................................................................................ 57 Method for assessing CNV calling performance ............................................................................... 58 CNV calling performance with simulated data .......................................................................................... 58 CNV calling performance with real data..................................................................................................... 58 Appendix B: Mask generation .............................................................................................................. 59 Compiling common translocation breakpoint list ............................................................................... 59 Compiling annotated segmental duplication regions ......................................................................... 63 Tools for generating mask BED files ................................................................................................. 63 Appendix C: Descriptions of output files ............................................................................................... 65 Output files from the de novo assembly pipeline ............................................................................... 65 Output files from RVP ....................................................................................................................... 67 Appendix D: In-depth description of the de novo assembly pipeline ..................................................... 69 Setting up a de novo assembly ......................................................................................................... 69 Key stages of the de novo assembly pipeline ................................................................................... 69 Runtime performance of the de novo assembly pipeline ................................................................... 74 Evaluation of de novo assembly results ............................................................................................ 74 Appendix E: Interpretation of inversion breakpoint calls ....................................................................... 75 Introduction ....................................................................................................................................... 75 SMAP output for inversion breakpoints ............................................................................................. 75 Inversion breakpoints report file ........................................................................................................ 77 Inversion confidence score ..............................................................................................................