Parse mapped scaffolds in BWA alignment

Question

[second_exon]

Hi all,

I'm learning bioinformatics from scratch, please bear with me, if I go wrong.

I sequenced (miseq) few of my BACs. I mapped these miseq reads on reference genome using BWA. My question is, how to parse out names of the scaffolds of my reference genome got mapped from alignment file?

Many Thanks

Answer 1

[GouthamAtla]

Here is SAM file format specification. You need to use samtools to view the contents of sam/bam file and then manipulate.

If you want to see the scaffolds:

samtools view <input bam> | cut -f3 | less

[second_exon]

Thank you! It worked!!