Scripts use to call and filter variants for all landrace dataset
callvariantsplate_20Apr2016.sh was used to call variants on the linux machine and finished on Nov 28 2016. the files are backed up on personal/tjamann/LRS_all28Nov2016
call variants with callvariantsplate_20Apr2016.sh
rename samples based on barcodes:accession/samples with rename.py renamefiles_py.py remane files in a directory based on a dictionary file
hwe filter only needs to be run if chr 2, 3, and 8 are included, not necessary for ZmCCT. hwe.rmd is a dependent file for the hwe filter
downstream analysis has code for figures in plos one 2017 paper
##Converting sample names Before you run the script, make a copy of the target vcf file and call it {}_rename.vcf. This script will overwrite the vcf! In order to change the sample names from DNA id to accession id use the following code: python src/rename.py -VCF data/GBS/vcf_files/combined_rename.vcf -DICT data/GBS_dict.txt