bam output file to psl file

[fahim]

Hi
I am doing short read alignment using bwa algorithm. I am able to convert the alignment output to .bam file.
Now, I want to see the alignments and how a read maps to the genome. In case of BLAT or other aligners such as bowtie, gives an output which contains information such as "readName, referenceChromosome, tStart, tEnd, qSize, etc ..etc..". I want the output in similar format.
Is there a way/command/software to do that through samtools.
Thanks in advance.
Fahim

[drio]

I suggest you spend some time getting yourself familiar with the format since (S|B)AM is the standard to store and represent alignments. It is here to stay.

Those specific fields you are looking for you can find in your BAM output from BWA. Take a look to the specification. Pay particular attention to section 1.4.

Furthermore, most of the downstream tools you may want to use are going to require alignments in (S|B)AM.