Run STACKS
sstacks
module inside R!
Inside the P folder (where the ustacks and the cstacks files are),
you should have:
3 Catalog files: the files created in
cstacks
and usually looking like this:
batch_1.catalog.alleles.tsv.gz,
batch_1.catalog.snps.tsv.gz,
batch_1.catalog.tags.tsv.gz
3 files for each samples: The sample name is the prefix of
the files ending with:
.alleles.tsv.gz, .snps.tsv.gz, .tags.tsv.gz.
Those files are created in the
ustacks
module.
run_sstacks(
P = "06_ustacks_2_gstacks",
M = NULL,
sample.list = NULL,
c = "06_ustacks_2_gstacks",
parallel.core = parallel::detectCores() - 1,
o = "06_ustacks_2_gstacks",
x = FALSE,
disable.gapped = FALSE,
v = FALSE,
h = FALSE
)(character) Path to the directory containing STACKS files.
Contrary to sstacks,
this argument can be use with sample.list (the s in sstacks)
Default: P = "06_ustacks_2_gstacks".
(character) Path to a population map file from which to take sample
names (this argument won't work if sample.list).
Advice: don't modify the default (please see details).
Default: M = NULL.
This is for the s option in
sstacks.
s: Filename prefix from which to load sample loci.
Here, you have 2 choices: 1. you leave empty and let the function use the
default:sample.list = NULL which will scan for the files in the
P folder given above. 2. you supply a character string of the
samples. This could come from the INDIVIDUALS_REP column of the
project info file, e.g. sample.list = project.info$INDIVIDUALS_REP.
(Please see details).
(character, path) Path to the catalog.
Default: c = "06_ustacks_2_gstacks"
(Integer) Enable parallel execution with num_threads threads.
Default: parallel.core = parallel::detectCores() - 1
output path to write results.
Default: o = "06_ustacks_2_gstacks"
Don't verify haplotype of matching locus.
Default: x = FALSE
Disable gapped alignments between stacks.
Default: disable.gapped = FALSE (use gapped alignments).
Print program version.
Default: v = FALSE
Display this help messsage.
Default: h = FALSE
sstacks
returns a .matches.tsv.gz file for each sample.
If lnl_dist = TRUE, the function will also return a
summary of catalog loci log-likelihood.
Computer or server problem during the sstacks ? Just launch again the same command, the function will start again, but only with the unmatched samples!
Some argument can't be use together:
Don't use these arguments together: M and sample.list/c.
You can't add samples to an existing catalog using a population map.
If you want to match new samples to an existing catalog, very easy,
just add the samples in the folder and let run_sstacks function find
the samples that were not matched to the catalog.
Catchen JM, Amores A, Hohenlohe PA et al. (2011) Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences. G3, 1, 171-182.
Catchen JM, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140.