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broadinstitute / viral-ngs

Viral genomics analysis pipelines
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in picard demux set max_mismatches=0 #960

Closed tomkinsc closed 5 years ago

tomkinsc commented 5 years ago

For more stringent demux, in picard demux set max_mismatches=0, from max_mismatches=1.

For larger runs, perhaps we should tolerate 1 mismatch by setting an alternative default here?