These are chat archives for dereneaton/ipyrad

6th
Dec 2015
Deren Eaton
@dereneaton
Dec 06 2015 18:39
:shipit:
So if I'm following correctly, the refmap stacks are being called with pileup, so they could pretty much skip to step7 from there?
Deren Eaton
@dereneaton
Dec 06 2015 19:26
Also, how hard would it be to use pileup to make base calls on the denovo data? Is that worth exploring? vsearch can output cluster data in sam format.
Deren Eaton
@dereneaton
Dec 06 2015 20:00
Also, if the refmap reads go through a separate path than denovo reads, i.e., not through step5 (consens_se.py) then we still need to apply similar filters to the reads (maxN, maxH, maxhaplos, mindepth), and to flag reads that have multiple hits to the reference.