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.
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This should still work thought I have not used it recently: http://genome.sph.umich.edu/wiki/BamUtil:_validate -
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?Comment
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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">Comment
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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!Comment
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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.Comment
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