diff --git a/bwa.1 b/bwa.1 index ee4e4f35..be63a5ab 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: @@ -302,7 +316,7 @@ Output all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments. .TP .B -C -Append append FASTA/Q comment to SAM output. This option can be used to +Append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (e.g. barcode) to the SAM output. Note that the FASTA/Q comment (the string after a space in the header line) must conform the SAM spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output. @@ -316,7 +330,7 @@ supplementary alignments. Mark shorter split hits as secondary (for Picard compatibility). .TP .BI -v \ INT -Control the verbose level of the output. This option has not been fully +Control the verbosity level of the output. This option has not been fully supported throughout BWA. Ideally, a value 0 for disabling all the output to stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for all normal messages; 4 or higher for debugging. When this option takes value