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Old 06-07-2010, 03:39 AM   #1
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Default BWA alignment for paired end reads


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.
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Old 06-07-2010, 06:19 AM   #2
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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.
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Old 06-08-2010, 03:11 AM   #3
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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 ?
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