GitHub - TonyKess/seaage_GWAS: Scripts used in seaage GWAS

Scripts used for submitting jobs on Compute Canada and R scripts for interpreting results for the sea age GWAS in Atlantic Salmon

REMINDER FOR TONY: Wrong NCBI genome ID is referenced in paper (it's charr - not the genome you aligned to), fix!

Name		Name	Last commit message	Last commit date
Latest commit History 59 Commits
01.cutadapt		01.cutadapt
02.align_newgenome		02.align_newgenome
03.deduplication		03.deduplication
04.dedup_index		04.dedup_index
05.indel_target_create		05.indel_target_create
06.indel_realignment		06.indel_realignment
07.ANGSD_bcf_bychromosome		07.ANGSD_bcf_bychromosome
08.pcangsd		08.pcangsd
09.bcf_to_vcf.sh		09.bcf_to_vcf.sh
10.beagle_impute		10.beagle_impute
11.ANGSD_GWAS		11.ANGSD_GWAS
12.selscan_xpnsl		12.selscan_xpnsl
13.vcftools_FST		13.vcftools_FST
README.md		README.md
analysis.1.FST_GWAS_rdachipcomp.R		analysis.1.FST_GWAS_rdachipcomp.R
analysis.2.polysel_prep.R		analysis.2.polysel_prep.R
analysis.3.Salmon_Seaage_polysel.R		analysis.3.Salmon_Seaage_polysel.R
analysis.4.polysel_results_compare.R		analysis.4.polysel_results_compare.R
analysis.5.xpnsl_compare.R		analysis.5.xpnsl_compare.R
analysis.chip1.GWA_popstructure.R		analysis.chip1.GWA_popstructure.R
analysis6.Gene_extract_and_MachineLearn.R		analysis6.Gene_extract_and_MachineLearn.R
analysis_chip.X.OLD.R		analysis_chip.X.OLD.R
meta.Filtering_and_prep.R		meta.Filtering_and_prep.R
meta.submit_jobs_bychrom.sh		meta.submit_jobs_bychrom.sh

Provide feedback