Cancer Sequencing Service Data File Formats File format v2.4 Software v2.4 December 2012 CGA Tools, cPAL, and DNB are trademarks of Complete Genomics, Inc. in the US and certain other countries. All other trademarks are the property of their respective owners. Disclaimer of Warranties. COMPLETE GENOMICS, INC. PROVIDES THESE DATA IN GOOD FAITH TO THE RECIPIENT “AS IS.” COMPLETE GENOMICS, INC. MAKES NO REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR USE, OR ANY OTHER STATUTORY WARRANTY. COMPLETE GENOMICS, INC. ASSUMES NO LEGAL LIABILITY OR RESPONSIBILITY FOR ANY PURPOSE FOR WHICH THE DATA ARE USED. Any permitted redistribution of the data should carry the Disclaimer of Warranties provided above. Data file formats are expected to evolve over time. Backward compatibility of any new file format is not guaranteed. 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RM_DFFCS_2.4-01 Table of Contents Table of Contents Preface ...........................................................................................................................................................................................1 Conventions .................................................................................................................................................................................................. 1 Analysis Tools .............................................................................................................................................................................................. 1 References ..................................................................................................................................................................................................... 1 Introduction ................................................................................................................................................................................4 Sequencing Approach ............................................................................................................................................................................... 4 Mapping Reads and Calling Variations ............................................................................................................................................. 4 Read Data Format....................................................................................................................................................................................... 4 Data Delivery ................................................................................................................................................................................................ 5 Data File Formats and Conventions .................................................................................................................................... 6 Data File Structure ..................................................................................................................................................................................... 6 Header Format............................................................................................................................................................................................. 6 Sequence Coordinate System ..............................................................................................................................................................10 Data File Content and Organization .................................................................................................................................................10 Identifier Map ............................................................................................................................................................................................12 idMap-[ASM-ID].tsv ............................................................................................................................................................................12 ASM Results .............................................................................................................................................................................. 13 Small Variations and Annotations Files..........................................................................................................................................13 Variations .....................................................................................................................................................................................................17 ASM/var-[ASM-ID].tsv.bz2 ..............................................................................................................................................................17 Master Variations .....................................................................................................................................................................................24 Normal Sample MasterVariations .....................................................................................................................................................25 ASM/masterVarBeta-[ASM-ID]-T1.tsv.bz2 ..............................................................................................................................25 Tumor Sample MasterVariations ......................................................................................................................................................34 ASM/masterVarBeta-[ASM-ID]-N1.tsv.bz2 .............................................................................................................................34 Individual Genomes’ Small Variations, CNVs, SVs, and MEIs in VCF Format ................................................................. 43 ASM/vcfBeta-[ASM-ID].vcf.bz2 .....................................................................................................................................................43 Comparative Results of Small Variations, CNVs, and SVs in VCF Format ........................................................................62 ASM/somaticVcfBeta-[ASM-ID]-N1.vcf.bz2 .............................................................................................................................62 Annotated Variants within Genes .....................................................................................................................................................81 ASM/gene-[ASM-ID].tsv.bz2 ...........................................................................................................................................................81 Annotated Variants within Non-coding RNAs .............................................................................................................................86 ASM/ncRNA-[ASM-ID].tsv.bz2 ......................................................................................................................................................86 Count of Variations by Gene ................................................................................................................................................................88 ASM/geneVarSummary-[ASM-ID].tsv ........................................................................................................................................88 Variations at Known dbSNP Loci .......................................................................................................................................................90 ASM/dbSNPAnnotated-[ASM-ID].tsv.bz2 .................................................................................................................................90 Sequencing Metrics and Variations Summary .............................................................................................................................94 ASM/summary-[ASM-ID].tsv .........................................................................................................................................................94 © Complete Genomics, Inc. Cancer Sequencing Service Data File Formats — ii Table of Contents Copy Number Variation Files ..............................................................................................................................................................98 Copy Number Segmentation ............................................................................................................................................................ 101 ASM/CNV/cnvSegmentsDiploidBeta-[ASM-ID].tsv .......................................................................................................... 101 Detailed Ploidy and Coverage Information ................................................................................................................................ 104 ASM/CNV/cnvDetailsDiploidBeta-[ASM-ID].tsv.bz2 ....................................................................................................... 104 Genomic Copy Number Analysis of Non-Diploid Samples Files ......................................................................................