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A collection of scripts, command lines, and instructions for the analyses performed in "Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm"

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SAP_PlantGenome

A collection of scripts, command lines, and instructions for the analyses performed in "Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm"

Please Cite:

Boyles, R. E., E. A. Cooper, M. T. Myers, Z. Brenton, B. L. Rauh, G. P. Morris, and S. Kresovich. 2016. Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm. Plant Genome 9.

Contents of the Repository:

TASSEL_SAP.md

The complete set of command lines run to call SNPs with the TASSEL 5.0 pipeline.

HapMap_Helpers

A repository of perl scripts and instructions for performing various functions on HapMap files, including filtering for missing data and minor allele frequency, as used in this paper.

formatConversion

A repository of perl scripts and instructions for converting between various file formats, including between the hapmap format and the fastPHASE format, as well as hapmap and STRUCTURE formats.

GWAS_Pipelines

Contains instructions and R code for running both the GAPIT and GEMMA programs as described in the paper.

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A collection of scripts, command lines, and instructions for the analyses performed in "Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm"

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  • Perl 86.2%
  • R 13.8%