Downsample to the same coverage as the lower coverage sample

[tleonardi]

Very different coverage between samples might causes troubles during GMM clustering.
At the moment we can downsample to a fixed coverage level, but it would be great to downsample each reference independently so that the sample with higher coverage is brought down to the same level as the sample with lower coverage.

[a-slide]

Are you thinking of doing it on a position per position fashion ?

[a-slide]

I would actually suggest to move the reference level downsampling from Whitelist directly to txComp at position level. The advantage of having it in the whitelist is that is saves time as we don't read the data discarded by the downsampling.