CalculateConsensus
CalculateConsensus.RdWe calculate the consensus information from the MAEGATK results. We set cells that have only alternative reads to 2 (Alternative). We set cells that have only reference reads to 1 (Reference). We set cells that have a mixture of alternative and reference reads to 3 (Both). We set cells that have no reads to 0 (NoCall).
Please note. Cells can have reads for the reference of a specific variant and no reads for the alternative. The cell can still have a reads for the other alternative alleles. Then the cell is still considered as 0 (NoCall) for this variant. For example: A cell has at position 3: 0 A reads, 53 T reads, 63 C reads, 148 T reads. For the variant chrM_3_T_A, the cell would have 53 reference reads, but also reads for other variants at this position. To make sure that there is no confusion, the cell is set to NoCall.