This file is the output of the pyRAD pipeline (pyRAD ".loci" format) ran on the raw sequence reads (accessible via GenBank, BioProject PRJNA382467) using the parameters which are given in the the pyRAD parameter file despoted in this repository ("pyRAD_parameters_file.txt"). It contains several technical replicates (which are denoted by the suffix "_R"), which are used in the study to determine the consistency of SNP calls
Loci file exported from clustering analysis performed in PyRAD. All molecular datasets referenced in...
This file outlines the exact steps to filter variant calls into a final SNP data set. Lines are com...
Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Ma...
This file is the output of the pyRAD pipeline (VCF format) ran on the raw sequence reads (accessible...
This is the parameter file containing all parameters used for de novo SNP calling using the pyRAD pi...
This file contains the Pyrad parameters file that was used to create the SNP dataset that was used (...
This files contains the SNPs that were used to identify redundant sequences. It is based on the file...
<p>First, the reads are demultiplexed and cleaned. Different types of references were built and the ...
SNP calls in HapMap format with basic filtering on missingness and allele frequency for 95 Junco sam...
This file contains the baseline sequence and polymorphism information for the 9410 RAD loci analyzed...
Raw SNP genotypes in PLINK format (i.e., .ped & .map file) before quality-control filtering
Locus file from pyRAD, clustering at 0.88 similarity, a minimum of 10 individuals per locus. This fi...
The filtered SNP dataset used in Barth et al. as PLINK/MERLIN/Haploview text genotype table (.ped), ...
Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Ma...
SNPs identifiers in PED format relative to the PED file containing genotypes based on RAD sequencing
Loci file exported from clustering analysis performed in PyRAD. All molecular datasets referenced in...
This file outlines the exact steps to filter variant calls into a final SNP data set. Lines are com...
Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Ma...
This file is the output of the pyRAD pipeline (VCF format) ran on the raw sequence reads (accessible...
This is the parameter file containing all parameters used for de novo SNP calling using the pyRAD pi...
This file contains the Pyrad parameters file that was used to create the SNP dataset that was used (...
This files contains the SNPs that were used to identify redundant sequences. It is based on the file...
<p>First, the reads are demultiplexed and cleaned. Different types of references were built and the ...
SNP calls in HapMap format with basic filtering on missingness and allele frequency for 95 Junco sam...
This file contains the baseline sequence and polymorphism information for the 9410 RAD loci analyzed...
Raw SNP genotypes in PLINK format (i.e., .ped & .map file) before quality-control filtering
Locus file from pyRAD, clustering at 0.88 similarity, a minimum of 10 individuals per locus. This fi...
The filtered SNP dataset used in Barth et al. as PLINK/MERLIN/Haploview text genotype table (.ped), ...
Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Ma...
SNPs identifiers in PED format relative to the PED file containing genotypes based on RAD sequencing
Loci file exported from clustering analysis performed in PyRAD. All molecular datasets referenced in...
This file outlines the exact steps to filter variant calls into a final SNP data set. Lines are com...
Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Ma...