Basic data extraction on bam files

[Philcolson]

I'm trying to get read counts for things like reference normal forward/reverse count, alternative/reference forward/reverse counts from a bam file. I've honestly read through so many forum posts and BioStar and I can't seem to find the answer. Any help would be appreciated.

[GenoMax]

This should still work thought I have not used it recently: http://genome.sph.umich.edu/wiki/BamUtil:_validate

[Philcolson]

I recall running into this site a bit ago. I'll give it another go. Thank you very much.

Are read counts not something typically used/had? I'm a bit of a novice in the art, but this strikes me as very important, no?

[swbarnes2]

Forward and reverse counts should be 50/50. You could get counts for all the flags, and tell from that how many go each way.

That's not a common thing to worry about.

You can't get "alternate" counts from the bam. If you make a vcf, the vcf is likely to have what you want in the DP4 value

##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">

[Philcolson]

After consulting with both you guys and a seasoned coworker, I've figured out what I needed I think. Thank you guys for the answers!

[bioinfo816]

I need suggestion to extract the chromosome or chromosome region (e.g. chr1: 100,000,000-200,000,000) without sorting bam file. Any idea related with this would be appreciated.