Call variants and identifies their somatic status (Germline/LOH/Somatic) using pileup files from a matched tumor-normal pair.
java -jar VarScan.jar copynumber [normal_pileup] [tumor_pileup] [output] OPTIONS
OPTIONS: --min-base-qual - Minimum base quality to count for coverage [20] --min-map-qual - Minimum read mapping quality to count for coverage [20] --min-coverage - Minimum coverage threshold for copynumber segments [20] --min-segment-size - Minimum number of consecutive bases to report a segment [10] --max-segment-size - Max size before a new segment is made [100] --p-value - P-value threshold for significant copynumber change-point [0.01] --data-ratio - The normal/tumor input data ratio for copynumber adjustment [1.0]
Note: The data ratio is intended to help you account for overall differences in the amount of sequencing coverage between normal and tumor, which might otherwise give the appearance of global copy number differences. If normal has more data than tumor, set this to something greater than 1. If tumor has more data than normal, adjust it to something below 1. A basic formula for data ratio might be something like ratio = normal_unique_bp / tumor_unique_bp where unique base pairs are computed as mapped_non_dup_reads * read_length.
OUTPUT chrom Chromosome name chr_start Region start position (1-based from the pileup) chr_stop Region stop position (1-based from the pileup) num_positions Size of the region in base pairs normal_depth Average normal sequence depth for the region tumor_depth Average tumor sequence depth for the region log2_ratio Log-base-2 ratio of: adjusted tumor depth over normal depth gc_content Estimated GC content of the region (0-100)
The raw regions reported by VarScan are delineated by drops in coverage or changes in the tumor/normal ratio, so there are many small, nearby regions with similar copy number. It is therefore recommended that raw VarScan copynumber output be processed with circular binary segmentation (CBS) or a similar algorithm, which will generate larger segments delineated by statistically significant change points. See the copy number calling section for details.