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falcon: Finding Allele-Specific Copy Number in Next-Generation Sequencing Data

This is a method for Allele-specific DNA Copy Number Profiling using Next-Generation Sequencing. Given the allele-specific coverage at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.