Perform GWAS analysis of sorghum data using tassel

[kshefchek]

HapMap file: https://datacommons.cyverse.org/browse/iplant/home/shared/terraref/genomics/derived_data/bap/resequencing/danforth_center/version1/hapmap/all_combined_genotyped_lines_SNPS_052217.recalibrated_vcftools.filtered.recode.hmp.txt

Phenotype data: https://drive.google.com/drive/folders/1K4OrHbaDvao7vrN0_V2yc0gD_wmvFXdC with more incoming via https://github.com/genophenoenvo/terraref-datasets/issues/24

Tassel: https://www.maizegenetics.net/tassel

Endpoints:

• SNP to phenotype associations with p-values and effect sizes
• Manhattan plot for all phenotype data
• Phylogenetic tree
• Documentation on this process

Follow up analyses (to become future tickets):

• Look for conservation of gwas snps in closely related species (looking at syntenic regions)
• Look for similar phenotype data in qtl datasets in planteome

[kshefchek]

Some notes on the data:

• Tall format contains time series data which I'm fairly certain tassel does not support. For now we'll take the final measurement
• Some measurements have the same time, eg leaf temperature. @MagicMilly doesn't think this is a resolution issue but rather there were multiple iterative measurements taken at once.
• Some measurements were only taken for a small subset of cultivars, eg leaf temperature was only measured for 12 culitvars. Should we add some filter for traits with < N cultivars (50?)
• Cultivars in the hapmap file are missing from the tall_format and vice versa. 67 cultivars from the hapmap file do not have phenotypes, bringing the cultivar sample size down to 295.
• Some measurements do not look like traits, eg lodging_present, harvest_lodging_rating. Should these be treated as factors and covariates or removed?

Tassel requires one of the following formats for phenotypes: Trait format: https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load#markdown-header-trait-format Phenotype format: https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load#markdown-header-numerical-data