BWA alignment for paired end reads

[AvinashP]

hi,

i am using BWA to align 115bp paired end solexa reads. I have the following doubts :-

1. Does BWA take the min and max insert sizes for paired end reads ?
2. What is maximum number of indels calculated by BWA ? Does keeping the indel as 3 will affect the performance ?
3. How do i get the unaligned reads seperately after using the 'sampe' command? The reads which are not paired and the reads which didn't map at all.
4. I plan to use samtools for SNP and indel detection. Can i get the reference as well as the consensus coordinate in the pile up format.

Any help for the above is appreciated.
Thanks

[lh3]

1. bwa infers it
2. hard to say for paired-end reads. could be up to 20bp in some cases
3. see sam format
4. it depends on what you exactly want.

[AvinashP]

Thanks, for your immediate reply.

For (2.) can we restrict the indels with the parameters -o and -e in the 'aln' step? What is the ideal value for these parameters given 115bp reads ?

4. i want the consensus coordinate also in the pileup format with the other fields. How to get it using samtools ?