---
file_transformation: 
  - Added header information to all files
  - SnpEff output was transformed from VCF to GFF using script provided at https://github.com/awilkey/vcf-to-gff-demo. 

changes: 
  - 2018-08-23: Creation of metadata and formatting of files for this repository
  - 2018-09-19: Made changes to all the VCF headers. Replaced whitespace with tabs in the sample line of the header (# CHROM) s/ \+/^I/g, replaced "Intergers" with "Interger", replaced "##FORMAT=<ID=PL,Number=3" with "##FORMAT=<ID=PL,Number=G", changed Gm to Chr. 
  - 2018-09-21: changed samples names USB003, USB004, USB005, etc to USB-003, USB-004, USB-005 in glyma.Wm82.gnm2.div4.Valliyodan_Brown_2021.USB-40x.vcf.gz, glyma.Wm82.gnm2.div4.G787.USB481.vcf.gz and glyma.Wm82.gnm2.div4.G787.USB481_nosoja.vcf.gz
  - 2019-05-14: Added SoyBase SNP IDs (A03.0000001 - A03.7869806) to glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.USB481.vcf.gz
  - 2019-08-12: Added glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.snpEff.gff3 file
  - 2020-01-03: Added alignment and phylogeny files: glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.sampled_25Kpos.tree and glyma.Wm82.gnm2.div.G787.sampled_25Kpos.fna
  - 2020-07-15: Added two new SnpEff output files: glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.snpEff_Gsoja.gff.gz & glyma.Wm82.gnm2.div.G787.snpEff_Gmax.gff.gz
  - 2021-04-15: Added citation information and doi.
  - 2021-04-27: add genome prefix
  - 2021-04-27: Change key from G787 to Valliyodan_Brown_2021
  - 2021-11-28: Add file with list of accessions, Wm82.gnm2.div.Valliyodan_Brown_2021USB481_accession_List.xlsx