I have data GBS derived from the UNEAK pipeline and I'd like to use the count.hmc file to remove SNPs from my HapMap.hmn file which fall below a given threshold (i.e. 20x).
I've done a fair bit of looking around and have not found a straightforward way to do this quality control.
Any suggestions of how to do this? It seems strange that the depth of coverage data is segregated from the rest of the data in the first place.
I've done a fair bit of looking around and have not found a straightforward way to do this quality control.
Any suggestions of how to do this? It seems strange that the depth of coverage data is segregated from the rest of the data in the first place.
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