diff --git a/bwa.1 b/bwa.1 index 206e32a..be63a5a 100644 --- a/bwa.1 +++ b/bwa.1 @@ -107,6 +107,8 @@ appropriate algorithm will be chosen automatically. .IR clipPen ] .RB [ -U .IR unpairPen ] +.RB [ -x +.IR readType ] .RB [ -R .IR RGline ] .RB [ -H @@ -256,6 +258,18 @@ Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these two scores to determine whether we should force pairing. A larger value leads to more aggressive read pair. [17] +.TP +.BI -x \ STR +Read type. Changes multiple parameters unless overriden [null] + pacbio: +.B -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 +(PacBio reads to ref) + ont2d: +.B -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 +(Oxford Nanopore 2D-reads to ref) + intractg: +.B -B9 -O16 -L5 +(intra-species contigs to ref) .TP .B INPUT/OUTPUT OPTIONS: