List of bash pipelines used in the analysis of variants in the ananassa genome. Basic toy analysis of individual genotypes. explore_ananassa_sql_snpchip.sh
Extended analysis of individual genotypes analyse_snp_chip_genotypes.sh
ananassa_nuc_div_by_chromosome.sh
Basic toy analysis of individual haplotypes. insert_ananassa_haplotypes.sh
Comparison of map-based and Impute-based haplotyping comparison_haplotyping_procedures.sh
Haplotyping of EMxFE, FLxCH, HAxRG EMR mapping populations with shapeit mapping_pops_haplotyping.sh
Troubleshooting haplotyping carried out in the file above. troubleshooting_haplotyping.sh
Testing shapeit settings to improve haplotyping improve_haplotyping.sh
Testing shapeit settings to improve haplotyping 2 improve_haplotyping2.sh
Testing shapeit settings to improve haplotyping based on vcf input. improve_haplotyping3.sh
Testing shapeit settings to improve haplotyping based on vcf input. improve_haplotyping4.sh
Testing shapeit settings to improve haplotyping based on vcf input. Testing using haplotypes from another population to improve phasing. improve_haplotyping5.sh
Extended analysis of individual genotypes 2, following fixing of mislabelled samples. analyse_snp_chip_genotypes2.sh
Local genotype association study for 10-20 markers around major QTLs for crown rot. crown_rot_qtl_markers_local_1.sh
GWAS for crown rot using PLINK and TASSEL (GUI) crown_rot_qtl_markers_gwas_1.sh
Re-analysis of GWAS and SBC genotypes focussing on plate provenance crown_rot_qtl_markers_gwas_plate.sh
Various checks of the ananassa snp chip database - QC. ananassa_db_qc.sh
Ananassa nucleotide diversity pipeline ananassa_diversity_pipeline.sh
GWAS pipeline - case vs. control (example: everbearer trait) gwas_case_control_pipeline.md
GWAS pipeline - quantitative phenotype (example: crown rot resistance) gwas_quantitative_pipeline.md