ReadDepth

Evaluate read depth in target regions, and obtain BAM file statistics used for calculating copy number

• Evaluate read depth (number of reads mapping to a genomic position) in WGS data for regions defined in PlotList. depthFilter.py will subsample the depth so that no more than about 10K data points are returned, no matter the region size.
• flagstat files, generated with the samtools utility, provide a summary of the number of reads in a BAM file. They are generated if they do not already exist (test appending .flagstat to BAM filename).
• Create summary table used to obtained copy number. Copy number at a given genomic position is estimated (in DepthDrawer.R) as 2 * read_depth / RD, where RD is average read depth across the genome, RD = num_reads * read_length / genome_length. num_reads is obtained from the BAM file directly.
• Similar statistics are obtained for RNA-Seq BAM files as well, to be used for RPKM calculations.