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bam file to bed fie

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.

sequence-alignment next-gen-sequencing
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updated by Ram Ram • written by 897598644 897598644

1 answer

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

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written by GenoMax GenoMax

So how could i get the position range?

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written by 897598644 897598644

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.

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written by GenoMax GenoMax

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