readStacks {polyRAD}

Import Read Depth from Stacks

Description

Using the catalog files output by cstacks and matches file output by sstacks, this function imports read depth into a RADdata object. If genomic alignments were used, alignment data can optionally be imported.

Usage

readStacks(allelesFile, matchesFolder, version = 2,
           min.ind.with.reads = 200,
           min.ind.with.minor.allele = 10, readAlignmentData = FALSE, 
           sumstatsFile = "populations.sumstats.tsv",
           possiblePloidies = list(2), taxaPloidy = 2L, contamRate = 0.001)

Arguments

allelesFile

Path to the "alleles" file from the Stacks catalog.

matchesFolder

Path to the folder containing "matches" files to import.

version

Either the number 1 or 2, indicating the version of Stacks.

min.ind.with.reads

For filtering loci. A locus must have at least this many samples with reads in order to be retained.

min.ind.with.minor.allele

For filtering loci. A locus must have at least this many samples with reads for the minor allele in order to be retained. For loci with more than two alleles, at least two alleles must be present in at least this many individuals. This argument is also passed internally to the min.ind.with.haplotype argument of MergeRareHaplotypes to consolidate reads from rare alleles.

readAlignmentData

If TRUE and version = 1, the "tags" file from the Stacks catalog will be read, and chromosome, position, and strand will be imported to the locTable slot of the output. It is assumed that the "tags" file is in the same directory as the "alleles" file. If TRUE and version = 2, sumstatsFile will be used for import of chromosome and position data.

sumstatsFile

The name of the file containing summary statistics for loci. Ignored unless version = 2 and readAlignmentData = TRUE.

possiblePloidies

A list indicating possible inheritance modes in the dataset. See RADdata.

taxaPloidy

A single integer, or an integer vector with one value per taxon, indicating ploidy. See RADdata.

contamRate

A number from 0 to 1 (generally very small) indicating the expected rate of cross contamination between samples.

Value

A RADdata object.

Note

This function has been tested with output from Stacks 1.47.

Author(s)

Lindsay V. Clark

References

Stacks website: http://catchenlab.life.illinois.edu/stacks/

Rochette, N. and Catchen, J. (2017) Deriving genotypes from RAD-seq short-read data using Stacks. Nature Protocols 12, 2640–2659.

Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., and Cresko., W. A. (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology 22, 3124–3140.

Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W., and Postlethwait, J. H. (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics 1, 171–182.

See Also

VCF2RADdata, readTagDigger, readHMC, readTASSELGBSv2, readDArTag

Examples

## Not run: 

# Assuming the working directory contains the catalog and all matches files:

myStacks <- readStacks("batch_1.catalog.alleles.tsv", ".", 
                       version = 1,
                       readAlignmentData = TRUE)

## End(Not run)