Reads that can align to multiple places

[ashwatha]

Hi,

is there a way to parse a BAM file and look for reads that can align to two different places on the reference genome equally well? For example, a read might be aligned to some coordinate in chr1, but maybe there is an equally good alignment elsewhere in the reference.

I believe a BAM file has provision for this kind of info to be set in one of the optional columns (XA:Z ?), but BWA doesn't seem to output this column by default. Is there a way to set an option to BWA to output this? Or is there a more obvious way to get this info?

thanks,
Ashwatha.

[simonandrews]

I don't know about BWA, but bowtie can be made to find these kinds of reads by using the --best and --strata options which will report only hits which match equally well. It should then be fairly simple to identify reads with more than one hit.

[ashwatha]

Thanks Simon. I will look at Bowtie. If anyone has a solution for this with BWA, I would be interested in that as well.