Jared Simpson
Jared Simpson
Thanks - I'll look into resolving these warnings.
Did you run out of memory with `-d 20000000`? Without `-a ropebwt` a memory inefficient algorithm is used. There is no 2 (or 4) billion nucleotide batch limit.
Whether it is worth using `-a ropebwt` depends on the read length distribution. I suggest sticking with the recommended parameters (not ropebwt, `-d X`). It shouldn't take very long.
Thanks for the update. I did see that paper from @rob-p's twitter - its on my to-read list :)
Interesting, thanks! I wouldn't have expected the runtimes to be (nearly) the same, but it is good to see.
Hi @hasindu2008, Thanks for looking into this. I don't have access to an ARM development machine so I have limited ability to help. This issue may have been caused by...
I'm with @cjw85. I think basing this on ALT would be simpler and more natural, as long as a sensible encoding of the ALT field can be found. I prefer...
In the ALT-based representation the number of haplotypes, and hence records in the ALT field/AF entries, is constrained by read depth and the combinations of modifications actually observed in the...
I've been thinking about this recently and want to raise a few issues that should be considered. The discussion so far has focused on situations where there is a variant...
I'm working on a specific application where the input library is low-ish complexity (not as bad as an amplicon, but not as good as WGS) so worried about the rate...