campanam/FAECES

Scripts to analyze noninvasive DNA from Mojave canid scats

FAECES*: Fast and Accurate Enrichment of Canid Excrement for Species (*and other analyses)

This repository contains scripts to analyze noninvasive DNA from Mojave desert canids using the FAECES* assay.

Citation

Please cite:
Parker, L.D., Campana, M.G., Quinta, J.D., Cypher, B., Rivera, I., Fleischer, R.C., Ralls, K., Wilbert, T.R., Boarman, R., Boarman, W.I. & Maldonado, J.E. 2022. An efficient method for simultaneous species, individual, and sex identification via in-solution SNP capture of low-quality scat samples. Molecular Ecology Resources. 22: 1345-1361. DOI: 10.1111/1755-0998.13552.

Prerequistes

canid_sex.rb requires Ruby >= 2.4.

Installation

Clone the repository: git clone https://github.com/campanam/FAECES
Make the scripts executable: chmod +x *.rb

Usage

canid_sex.rb performs sex determination using a previously called SNP VCF of the ZFX/ZFY region. Options include:

-i, --input [FILE]       Input VCF file of SNPs in the ZFX/ZFY region. *Required*.
-s, --species [FILE]     Species assignment file. *Optional and Experimental*.
-k, --males [FILE]       List of known males to empirically calculate Y-allele frequency. *Optional*.
    --mean               Infer Y frequency using mean Y frequency across known male samples
-z, --zscore [VALUE]     Infer mean Y frequency from known male samples and set z-score bound
    --min                Infer Y frequency using minimum Y frequency across known male samples
-m, --minalleles [VALUE] Minimum number of allele reads to call sex (Default = 10)
-y, --yfreq [VALUE]      Expected Y-allele frequency (Default = 0.5). *Required if not inferred from known males*.
-a, --alpha [VALUE]      Alpha value for statistical significance (Default = 0.05).
    --yx [VALUE]         Use specified Y-X allele ratio to determine sex rather than statistical test.
-Z [VALUE]               Use z-score cut-off to determine Y-X ratio.
-h, --help               Show help

The males file is a simple text list. See canid_males_ZFX.txt for an example.
The species file is a CSV in the format sample,species. Use 'KF' to denote kit fox and use kit-fox-specific Y alleles. NB: this option is experimental and has not been fully tested or debugged.

The final sex determination datasets are available here. To obtain the raw sex determinations, use the following commands:

Coyotes: ruby canid_sex.rb -i Coy_ZFX.raw.vcf -k canid_males_ZFX.txt --min > Coy_ZFX_sex.tsv
Kit foxes: ruby canid_sex.rb -i KitFox_ZFX.raw.vcf -k canid_males_ZFX.txt --min > KitFox_ZFX_sex.tsv