Erik Garrison

The coordinates would be relative to the window, or maybe to any underlying repeats. The learner can't seem to figure out that there is a repeat and the sequence is...

By the way, we do retain information from the alignments to the graph, so we're not necessarily throwing these all out. We might just want to mark which reads don't...

Another example:  In tview it's clear that the reads supporting the reference aren't fully overlapping the repeat. 

In freebayes we can exclude these. In fact, although that isn't default there is discussion and support from folks like @chapmanb that we should do so by default as it...

In the last case the graph feature doesn't help us because we've inappropriately broken the site into two. That's another problem that I find a bit confusing... I thought I'd...

It's not the right thing to do to call reference. At these examples we have non-reference genotypes.

Thanks @ocxtal, I had been thinking about this after posting it and came to a similar conclusion. But, I had still thought that it might make sense to use libgaba...

I am looking into using ksw2. I guess I will run it along the edlib alignment path, varying the bandwidth and xdrop as suggested by the alignment path. It seems...

``` vw -d ~/NA12878_V2.5_Robot_1.1.hhga.gz --binary --passes 20 -q ha --ngram h5 --nn 100 -c -b 25 -f ~/ngram5hnn100_robot1.model --compressed ``` ``` vw -d ~/NA12878_V2.5_Robot_1.1.hhga.gz --binary --passes 20 -q ha --nn...

``` vw -d ~/NA12878_V2.5_Robot_1.1.hhga.gz --binary --passes 1 -q ha --ngram h2 -c -b 18 -f ~/ngramh2b18passes1_robot1.model --compressed ```