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Somatic Genotyping
The Somatic Genotyping module simultaneously analyzes 2 BAM files with read alignments, 1 for a normal sample and 1 for the tumor. Mantra assumes that each BAM file contains reads from only one sample and tracks the sample membership of each read through the workflow.
The Somatic Genotyping module attempts to estimate the probability of a variant being somatic given the read coverage in normal and tumor samples. To do so, it gathers a pool of breakpoint-associated reads from each sample and realigns them to the reference and putative somatic allele to estimate allele support from each sample.