BWA / Samtools with multiple references

[keebs42]

Hi all,

Does anyone have experience using BWA to align reads to multiple reference sequences? I am aligning reads from an exon capture run to a transcriptome reference and I'm wondering if a read will only be aligned to a single transcript. Ideally I would want the alignment reported for all transcripts (for multiple splicings) that the read aligns to equally. I'm also curious to how the pileup file would be printed if I carry the bwa sam output from this alignment step through the samtools pipeline... ie will all of the references (each transcript in my case) be placed in a single pileup file, or is there always only one pileup file reported per reference?

Thanks for your help,
Jon