-max_locus_stacks

[Steve]

Hi,

I have a quick question just to confirm my understanding of using the -max_locus_stacks option.

I have high coverage of a pooled population (containing 4 haplotypes) and I want to run it through ustacks with the -d option on and --max_locus_stacks set to 4. I basically just want to end up with a set of loci that will act as a reference in further analysis. With these settings only, loci with 5 or more stacks will be shunted to the deleveraging algorithm to be broken down and does the deleveraging algorithm work on the basis that their should be 4 haplotypes?

If I were to turn off the deleveraging algorithm would any loci having 5 or more stacks not be included in the .tags.tsv file? 

Cheers,

Steve  

[Julian Catchen]

Hi Steve,

If you turn on deleveraging, stacks may be broken down below the level specified
by --max_locus_stacks, however, there is no guarantee what depth those stacks
will be, only that they will be <= max_locus_stacks.

If you do not turn deleveraging on, then any stack with > max_locus_stacks will
be blacklisted and no attempt to break down stacks will be made.

All stacks will be output into the *.tags.tsv file, however those that are
blacklisted will have a flag set to "1" in their consensus sequence line in the
file so they can be ignored. The website FAQ lists which column this is in.

Best,
julian