bam file to bed fie

Question

[897598644]

Excuse me:

I got bam file from targeted resequencing. So how do I know the start and end region from the bam file?

Thanks for your help.

Answer 1

[GenoMax]

You won't know the exact boundaries since some reads will extend beyond the targeted region(s). But you should get a rough idea.

[897598644]

So how could i get the position range?

[GenoMax]

You can parse the BAM file and look at the POS/TLEN fields. If this is a common genome, with a BED annotation file available, then you could use coverageBED from BEDTools to get a rough idea of what regions are covered.