Exome caputure: masking the non-genic sequences before aligning ?

[lindenb]

Hi all,

I'm about to map a set of short reads after an exome capture.

I wonder if it would be worth to replace all the non-genic genomic sequences (using ucsc 'knownGene' ) with 'N'.

Wouldn't it speed up the alignment with BWA ? What would be the other possible consequences ? Has it ever been done before ?

Many thanks

Pierre

(copied from : http://biostar.stackexchange.com/questions/4413 )

[krobison]

The main consequence of removing information is increasing the risk of false alignments -- i.e. BWA may decide to make an imperfect & incorrect alignment which is the best it can make with your masked database, but with an unmasked one it would find a better (and correct) alignment. So, you may have false variant calls as a result.

BWA is very, very fast -- unless you have heaps of data I doubt you'll really find the speed benefit valuable. If you do need to speed up, an alternative strategy is to first align with Bowtie (which is even faster), saving the unaligned reads to files (this is an option) -- now run those through BWA. There is still a risk that Bowtie & BWA might have aligned a given read differently, but that is (in my guess) a smaller risk than masking out most of the genome.