How to display the sequence of each aligned fragment?

[shuang]

I used bwasw to align my Illumina reads to a reference genome. Then I use Samtool to pileup to an output.

In the output, it only shows hetero or homo on the SNP base. But I also want to see thea ctual sequences of aligned fragments, queried reads and aligned genome fragments.

How do I do it?

[sdvie]

To see the sequences of the reads that were aligned, have a look at the .sam file that is output by bwa directly. See here for more information on what you can see in a .sam file:
http://samtools.sourceforge.net/SAM1.pdf

Alternatively, or to get a more visual idea of the alignments, you can convert your .sam to .bam, sort and index it using samtools and then use samtools tview. It opens a simple alignment viewer that allows to jump to any position in the reference.

cheers!