I'm wondering exactly how bowtie2 calculates the read mapping qualities shown in the output SAM file. The documentation makes it very clear how the internal mapping score is calculated, and how you can customize it (e.g., setting various penalties for mismatches and indels), and it says that this is used to calculate the actual mapping quality, but I can't find anywhere that shows exactly how the mapping quality is ultimately calculated.
Does it use the same heuristic formula as in MAQ? Here's the paper I know about:
Li H, Ruan J, Durbin R. (2008) "Mapping short DNA sequencing reads and calling variants using mapping quality scores." Genome Res. 18:1851--1858.
Many thanks for your help,
Michael
Does it use the same heuristic formula as in MAQ? Here's the paper I know about:
Li H, Ruan J, Durbin R. (2008) "Mapping short DNA sequencing reads and calling variants using mapping quality scores." Genome Res. 18:1851--1858.
Many thanks for your help,
Michael
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