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Old 06-07-2010, 04:39 AM   #1
AvinashP
Junior Member
 
Location: India

Join Date: Jun 2010
Posts: 7
Default BWA alignment for paired end reads

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
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