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natsuhiko / rasqual

Robust Allele Specific Quantification and quality controL
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MAF filtering with -a uses > rather than >= #34

Closed kwcurrin closed 4 years ago

kwcurrin commented 4 years ago

Hello,

When setting -a to 0.1 to get MAF >= 10%, the smallest and largest allele frequencies in my RASQUAL output files are 0.125 and 0.875, indicating that the MAF is 0.125. I have 20 samples, so 0.125 is the next highest MAF after 0.1. Would it be possible to change -a to select >= value rather than > value? Alternatively, updating the documentation to suggest using a value slightly lower than the target MAF could be a good work around. For example, -a 0.099 if 0.1 is required.

Thanks!

Kevin

natsuhiko commented 4 years ago

Hi Kevin,

Thanks for pointing out. I updated the code.

Best regards, Natsuhiko