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Supplemental Material for Boatwright et al., 2021
dataset
posted on 2021-02-25, 17:44 authored by J. Lucas Boatwright, Zachary W. Brenton, Richard E. Boyles, Sirjan Sapkota, Matthew T. Myers, Kathleen E. Jordan, Savanah M. Dale, Nadia Shakoor, Elizabeth A. Cooper, Geoffrey P. Morris, Stephen KresovichSupplemental figures, tables and the CP-NAM VCF file. GBS were processed using Tassel version 5.2.52 (Bradbury et al.2007) following the GBS version 2 pipeline procedures (Glaubitz et al.2014). Tags were63aligned to the BTx623 version 3.1 annotated reference genome (McCormick et al. 2018), obtained from Phytozome (Goodstein et al. 2012), using BWA version 0.7.17 (Li and Durbin 2010). Beagle version 5.1 was used to impute missing genotype data in the variant call format (VCF) file resulting from the Tassel pipeline (Browning et al. 2018). The effects of SNPs were predicted using snpEff (Cingolani et al.2012).
