More than one possible mapping place for a read
When there is more than one possible mapping place for a read, being both places of equal score,
Where 'bwa mem' mapper finally maps it?
What about the mapping quality scores for the read?
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WouterDeCoster
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biotech
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biotech
1 answer
It depends on your settings, but I think the default is multimapping the reads. So the same read will be present in multiple locations. Mapping quality will be 0 (meaning the read maps equally well in multiple places).
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WouterDeCoster
You are giving me doubts about my answer. ;-) Might very well be possible that random mapping happens.
Well, the easiest approach to settle this would be to test it. Have a single multimapping read, map it, count the reads in the samfile.
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