Hi,
I wonder is it possible for BWA to avoid search for suboptimal alignments? I want only equally best hits to be reported.
And could I somehow limit the possible number of equally best hits that would be reported in X0 tag? It could be done for XA, but for X0... E.g., read1 could be equally mapped to the 100 positions. Will BWA report 100 in the X0?
thanks!
I wonder is it possible for BWA to avoid search for suboptimal alignments? I want only equally best hits to be reported.
And could I somehow limit the possible number of equally best hits that would be reported in X0 tag? It could be done for XA, but for X0... E.g., read1 could be equally mapped to the 100 positions. Will BWA report 100 in the X0?
thanks!
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