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Load GBS Genotype Experiment

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The Triticeae Toolbox edited this page Jul 12, 2018 · 1 revision

When loading over 100K markers, the web based tools are too slow (over 24 hours) so it is necessary to load the data using command line scripts.

  1. load_gbs_bymarker.php database input_file trial_code example "php load_gbs_bymarker.php T3wheat all_chr_300acc_SNPs_min50acc_rmMultiAllele_addHeader.vcf.tassel HWWAMP_GBS_2014" "php load_gbs_bymarker.php T3wheat all_chr_300acc_SNPs_min50acc_rmMultiAllele_addHeader.vcf.rrblup HWWAMP_GBS_2014"

  2. cron/create-allele-byline-exp.php trial_code

  3. load_gbs_frequencies.php database input_file trial_code example "php load_gbs_frequencies.php T3wheat all_chr_300acc_SNPs_min50acc_rmMultiAllele_addHeader.vcf.frequencies HWWAMP_GBS_2014"

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