Deleveraging Algorithm

[Stephen]

Hi,

I would just like to double check something. If I do not enable the
deleveraging algorithm, then will ustacks basically output all
haplotypes identified at a particular locus?

Cheers,

Stephen

[Julian Catchen]

Hi Stephen,

When the deleveraging algorithm is turned off in Stacks (by omitting the '-t'
option to denovo_map.pl or the '-r' and '-d' flags in the ustacks program) all
loci will be reported, no matter how many stacks were merged together to create
that locus. In addition, stacks with extremely high depth (as many as tens or
hundreds of thousands of reads) will not be blacklisted either (this is the '-r'
flag in ustacks). The typical result will be tags with high coverage with scores
of SNPs called in them. These typically, though not always, result from
repetitive regions in the genome that are all slightly different from one
another and are merged together.

There are flags in the *.tags.tsv file that indicate when a stack has been
broken down so that these loci can be ignored. Stacks that are blacklisted by
the deleveraging algorithm won't be loaded into a catalog.

julian

--
Julian M Catchen, Ph.D.
Institute of Ecology and Evolution
University of Oregon
--
jcat...@uoregon.edu
http://www.uoregon.edu/~jcatchen/

[Stephen Byrne]

Thanks Julian,

I have to work with pooled samples and I just want to get an idea of the number of alleles present when I have 2 and 3 SNPs in a tag. The alleles.tsv generated in ustacks looks like i is giving me this information. 

Cheers,

Stephen

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