Obtaining reference identical reads from a BAM file

[Sakti]

Hi guys,

This forum is awesome. I recently just started using software for seq data analysis. One question I have right now is how can I obtain the reads that map with 100% identity (no mismatches) to a reference genome. I have BAM files available, and was thinking that SAMTools is the way to do it, but I haven't figured it out yet.

If someone could point me to a useful reference or give me some guidance I'll be extremely grateful.

Thanks!

-Sakti

[swbarnes2]

You could use grep on the .sam file. There are a couple of entries that might be in your sam file that would indicate what the distance is between your read and your reference, and what the actual differences are between your read and your reference. If the NM value equals 0, then there are no differences (though you might also want to check the CIGAR entry, to see that there was no clipping of the read).

[Sakti]

Thanks for the help!! I ended up using MUMmer to get all identical sequences. I guess it was more straightforward than using the BAM alignments...