sequence alignment report

[slny]

I have sequence alignments of a few samples. I'd like to see the sequence difference between these samples compared and the reference genome.

Is there any tool that I could import the alignment data and reference genome sequence, then I could get a report telling me the difference between the samples and the reference genome?

Thanks a lot in advance!

[epigen]

If your alignment is in BAM format, samtools mpileup and bcftools is likely the best choice:
http://samtools.sourceforge.net/mpileup.shtml
You can get SNPs and Indels in vcf format for each sample, then use e.g. BEDTools http://code.google.com/p/bedtools/ for comparisons between the samples.

[slny]

Thanks a lot for your responses. It's very helpful.

Is bcftools included in samtools?

[slny]

Just found bcftools is also included in samtools.