Hello,
Here I have a question about downsample_to_coverage in HaplotypeCaller. I found -dcov cannot be used in HaplotypeCaller and I tried to change the values of parameters maxReadsInRegionPerSample and minReadsPerAlignStart to change the coverage level, but what I got the coverage of result files is still default coverage level.
so I wanna ask what parameter in HaplotypeCaller could change the level of coverage? if they are above two parameters, then how could I increase the downsample_coverage?
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downsample_to_coverage in HaplotyperCaller
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