BWA align contigs with Clustal-like output

Question

[biotech]

Is it possible to have BWA align contigs to reference and have output visualised via IGV/Tablet with Gaps and SNPs highlighted?

I'm trying this strategy because I need to visualise alignment of 10-20 regions of the reference genome but don't have this regions in separated fasta files for other strains we want to identify SNPs/indels for some reference coordinates. All bacterial data is already assembled.

[GenoMax]

You may be able to use Mauve for this without doing alignments with bwa.

Answer 1

[Devon Ryan]

Is it possible to have BWA align to contigs to the reference...

Yes

...and have output visualised via IGV/Tablet...

BAM format

...with Gaps and SNPs highlighted?

In IGV differences are colored by default. Indels are also marked. I assume Tablet does something similar, I've never used it.