What is default paprameter of BWA mem mapping

Question

[Bioinfonext]

Please Discuss the default parameter setting of BWA mem.

I used bbmap and BWA mem with default setting to map raw reads to CDS transcripts and I found that BWA is able to map more number of reads in comparison to bbmap.

I know in bbmap default setting is 76% identity but not aware about BWA mem.

Thanks

[Brian Bushnell]

By default, BWA produces multiple alignments per read, while BBMap does not unless you add the "ambig=all" flag. Be sure that you are counting correctly - the number of alignments produced is not the same as the number of reads that map. The difference is particularly large for transcriptome mapping because of all the duplication due to isoforms.

Answer 1

[vmicrobio]

Default seed is 19 bp, you can change it with '-k' option

bwa mem -k 30 reference.fasta file.fastq > alignment.sam

seed will be now 30 bp

Answer 2

[Jenez]

I would take a guess and say that the default settings for each parameter can be found on the documentation page for bwa mem here.

See the values within [ ] for the default parameters.