Downsampling Experiment
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Hello!

Trying to downsample in an orderly fashion in the name of experimentation, and in doing so would like to specify just one chromosome for the experiment - so I picked chromosome 17 with -L and a coverage of 30x with -dcov 30. This came up:

ERROR MESSAGE: Locus-based traversals (ie., Locus and ActiveRegion walkers) require a minimum -dcov value of 200 when downsampling to coverage. Values less than this can produce problematic downsampling artifacts while providing only insignificant improvements in memory usage in most cases.

I was hoping to poke through results from using the HaplotypeCaller with many different simulated depths of coverage for several samples. I read that one can use -dfrac instead, and that it might even be more appropriate, though I was hoping to find out what level of coverage led to what level of results and using -dfrac feels much less specific as it appears to toss a fraction of however many reads where at a given position, rather then tossing reads over a certain coverage. Thus with -dfrac, I could say that my sample had an average of 30x for this chromosome and I tossed half so theoretically I've simulated 15x depth of coverage...

Which approach would be more representative of reality? Using -dfrac to simulate a certain depth of coverage, or -dcov assuming I didn't have the 200 restriction?

Thanks for any help/discussion! -Tristan


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