I am interested in extracting strand info at any or all given positions from an alignment. The purpose is to get info about strand bias in a haploid organism. I know GATK provides strand bias in their genotyper output, but I want the actual counts...for example, at position 500 in my reference, 250 are derived from one strand and 250 are from the other. I'm not concerned about the call, per se, rather the value associated with the calls at that position.
If this makes sense to anyone and you have some ideas or a tool that already can accomplish this task, let me know.
Thanks...
If this makes sense to anyone and you have some ideas or a tool that already can accomplish this task, let me know.
Thanks...
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