The following consensus calling procedure is used to calculate a consensus for BAM files, and to correct the consensus when converting an AMOS file that was created by Velvet into an ACE file. Consensus BaseSearch for each position for forward and reverse reads for a base:
If different bases are found for forward and reverse reads, unite forward and reverse and repeat algorithm above on this single list. Finally, do an ambiguity check:
Consensus Base QualityConsensus gaps have always quality 0. If consensus is not a gap, use MIRA-Like consensus quality calculation: Best quality for a base in a direction makes basic rate = 100% add to this: 10% of next best base quality. Same procedure for other direction (if available), then add both qualities In general, the values are almost the same (mostly a tad higher) as with the more complicated (and time consuming) old variant. Cap at 90. Example: + A 30 -> 30 \ + A 20 -> 2 \ + A 20 / = 32 \ + A 20 / \ > = 60 - A 26 -> 26 \ / - A 20 -> 2 > = 28 / - A 15 / (+ = forward. - = reverse) Uncovered Reference Genome Positions in BAM FilesIf the reference genome has regions that are uncovered in the genome under study, those gaps are deleted in the resulting consensus sequence and juxtapositional covered regions are concatenated. This rule applies also for FASTA files that are exported. |