Process data generated by DArT-Seq for SNP selection and format for relatedness calculations and pedigree reconstruction
Filter SNP data based on the following parameters:
-Minor allele frequency -Call rate -One SNP per contig (linkage disequilibrium) -Errors between duplicate samples -Hardy-Weinburg equilibrium
Format data for use with the following programs:
-FRANz -Cervus -Coancestry -Plink
Create files with subsampled number of snps and individuals for exploratory power analyses
Files
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SNP_filtering_1.R : filters raw SNP data and formats for each program
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Subsampling_Schemes_2.R : generates subsampled files for power analyses
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batch_plink.bat : batch script for running plink subsamples
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Genome_results_3.R : concatenate results from plink genome analyses and produce heatmaps