---
file_transformation: 
  - Convert GmHapMap_Gt.gz into a VCF file and add SoyBase names. 
	- 1) Add REF and ALT alleles
		- took the first 4 columns fo GmHaMap.VarType.gz, which contain CHROM, POS, REF, ALT and pasted this information to GmHapMap_GT
		- used AWK '{(if $2 != $6) print "no" }' to make sure the paste worked and the information is the same.
		- removed columns 5 & 6, which were duplicate CHROM and POS columns 
		- used GmHapMapGt-to-vcf.py to convert into VCF file format
		- replaced the header the script created with the header from GmHapMap.var.ann.gz
	- 2) Assign and Add SoyBase names#
    - use script assign_names.awk (available at SoyBase Github) to assign names (A01-00000001) to each SNP and add them to the VCF file. 
  - For glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.haplotypes_by_gene.hmp, combined separate files-per-gene from haps/ from Dr. Torkamaneh into a single file, adding gene name in column 1
  - For glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.genotypes_by_gene.hmp, combined separate files-per-gene from haps/ from Dr. Torkamaneh into a single file, adding gene name in column 1

changes: 
  - 2019-05-07: Creation of metadata and formatting of files for this repository
  - 2019-07-12: Creation of VCF file glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.NonSynSNPs.vcf.gz, a VCF file only containing Non-Synonymous SNP locations. Using the file GmHapMap.var.ann file produced from SnpEff, SNPs that were annotated as having a HIGH or MODERATE effect were assigned as Non-Synonymous SNP locations. These locations were then extracted from the original VCF file glyma.Wm82.gnm2.div.HVCP.SNPData.vcf.gz to produce this new VCF file. 
  - 2020-01-06: Added files: glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.genotypes_by_gene.hmp.gz glyma.Wm82.gnm2.div.HVCP.haplotypes_by_gene.tsv.gz glyma.Wm82.gnm2.div.HVCP.loss_of_function.xlsx.gz . See file transformation notes above.

  - 2021-04-27: add genome prefix
  - 2021-04-27: Change key from HVCP to Torkamaneh_Laroche_2019