Data from: Assessing the potential of genotyping-by-sequencing (GBS)-derived SNPs to identify the geographic origins of intercepted gypsy moth (Lymantria dispar) specimens: a proof-of-concept study

Picq S, Keena M, Havill N, Stewart D, Pouliot E, Boyle B, Levesque RC, Hamelin RC, Cusson M

Date Published: September 25, 2017

DOI: https://doi.org/10.5061/dryad.01s00

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Title Picq_et_al_2017_raw_and_filtered_SNP_data
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Description The file contains all of the SNP data used in our article. The files named HapMap.fas.txt, HapMap.hmc.txt and HapMap.hmp.txt were obtained with the de novo UNEAK pipeline and respectively contains sequence of the SNP tag/read, the tag/read counts of each allele of the SNPs in each individual and eventually the genotypes. These files were obtained with the following default parameter settings: minimum tag count c = 5, error tolerance rate in the network filter e = 0.03 and minimum minor allele frequency mnMAF = 0.05. The last file named LymantriaD_Picq_et_al_80%_coverage_MafHeHw_LD_20170920.vcf present the 2327 SNPs obtained after the different SNP filtering steps (see Table 2 in our article). The 133 outlier SNPs are present in this file.
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When using this data, please cite the original publication:

Picq S, Keena M, Havill N, Stewart D, Pouliot E, Boyle B, Levesque RC, Hamelin RC, Cusson M (2017) Assessing the potential of genotyping-by-sequencing (GBS)-derived SNPs to identify the geographic origins of intercepted gypsy moth (Lymantria dispar ) specimens: a proof-of-concept study. Evolutionary Applications, online in advance of print. https://doi.org/10.1111/eva.12559

Additionally, please cite the Dryad data package:

Picq S, Keena M, Havill N, Stewart D, Pouliot E, Boyle B, Levesque RC, Hamelin RC, Cusson M (2017) Data from: Assessing the potential of genotyping-by-sequencing (GBS)-derived SNPs to identify the geographic origins of intercepted gypsy moth (Lymantria dispar) specimens: a proof-of-concept study. Dryad Digital Repository. https://doi.org/10.5061/dryad.01s00
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