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Cross Species Validation
I have a number of BAM files that have been blasted against hg19 using UnifiedGenotyper to find variants. The data comes from a human/mouse chimera. We have a few dozen high quality and interesting SNPs. Now I need to verify that the reads are not mouse genes that fit the human genome. I am not exactly sure how to do this but I am looking at
1) Running a walker (LocusWalker??) over the interesting locations - gathering the SamRecords and writing them to a SAM file or just keeping them in memory - the set is not large.
2) Running a ReadWalker over the BAM representing the fit to the mouse genome and seeing if the reads fit a consistent location and if the detected SNPs are present in the mouse reference.
There may be a better way to do this but I am pretty new to GATK - I suspect writing a couple of custom walkers is the simplest - To say published samples , say CountLocusWalker, are crude is an overstatement. Assuming I write my own walkers - how do I access the reference genome in the region of a GenomeLocation and how do I go from PileupElement to SAMRecord.
Or am I doing this all wrong and there is a better way???