Computational time for different methods applied to Dataset II.

a The LRR and BAF data can be extracted from the final report generated by Illumina GenomeStudio.b BAM file is required by ExomeCNV for calling CNV, while VCF file is optional and used for calling CN-LOH. BAM file is processed by GATK.c BAM file is processed by a perl script distributed along with CNAnorm.d BAM file is processed by SAMtools.e Computational time is unified to single thread CPU time in minute. The list values are average time across samples with standard deviation included in parentheses.Computational time for different methods applied to Dataset II.