Content of the Reference Library provided with WGS Extract v4 Installation:

You can relocate the library (this folder) with a setting inside the program.
 It is often helpful to move the folder and its content before setting a new
  location in the program.  The installer will also pick up on this relocated
  setting and act accordingly. The majority of space will be taken up by the
  Reference Genomes; none of which are installed until you request it in the
  Library.*** manager script.

Liftover Chain file (ucsc.edu, T2T):
-- used by Liftover in the Microarray generator when starting with a
   Build 38 model BAM
* hg38ToHg19.over.chain.gz  (and corresponding .gzi index file)
* chm13v2-{grch38, hg19}.chain for T2T chm13v2 to Build38 and 37
* {grch38m hg19}-chm13v2.chain for Build 38 / 37 to T2T chm13v2

Y Chromosome SNPs file (yBrowse.org):
-- used by Y DNA VCF file generator
* snps_hg38.vcf.gz, snps_grch38.vcf.gz -- Build 38 files 
    in chrN and N nomenclature; respectively
* snps_hg19.vcf.gz, snps_grch38.vcf.gz -- Build 37 files 
    in chrN and N nomenclature; respectively
(and corresponding .gzi and .tbi index files)
(note: original hg19 had some errors and had not been updated since 2017. 
  Now corrected. Original left here with added .orig suffix)

Exome BED Files for determing WES regions ():
-- Original TruSeq from Illumina for Build 37:
        https://support.illumina.com/downloads/truseq-exome-product-files.html
   Build38 form converted from TruSeq by BioBank:
        https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=3803
* TruSeq_Exome_TargetedRegions_v1.2.bed -- Build 37 chrN nomenclature
* TruSeq_Exome_TargetedRegions_v1.2_GRCh.bed -- Build 37 N nomenclature
* xgen_plus_spikein.GRCh38.bed, xgen_plus_spikein.GRCh38.GRCh.bed -- 
    Build 38 chrN and N nomenclature

Y Chromosome BED files (with mito added):
-- for use in the WES buttons on Y-only (or Y and MT only) BAM files.  We use
   the Phylogenetic Tree of Haplogroup communiy regions BED instead of the Y 
   Exome BED. Original is from a spreadsheet of HG38 regions created by
   David Vance from various sources (Ian McDonalds paper, yFull data, FTDNA
   data). See the user manual for more details.
* BigY3_hg*.bed - various Y BED files specific to FTDNA BigY-700 test
* CombBED_McDonald_Poznik_Merged_hg*.bed - various BED files as mentioned
   above; as created from David Vance's spreadsheet

Genomes Seed definition file:
--- copied into Genomes/ on first use. Used by Library and 
    get_and_process_refgenome.sh scripts
* seed_genomes.csv

Genomes/:
-- Starts as an empty folder.  Filled by Library.*** command and Ref Genome
   Library scripts in scripts/:
* process_refgenomes.sh -- sript to index any available reference 
     genomes (called by get_and_process_refgenomes.sh)
* compare_refgenomes.sh -- script to compare two reference genomes
     based on extracted stats
* get_and_process_refgenome.sh -- script to individually download and
	 process each reference genome for use in the program.  Called by the
     Library.* tool and the WGS Extract program itself.	 
* bwa-kit-gen-ref.sh   -- modified (updated, corrected) script from bwa-kit
     to make 1K Genome project reference models (aka hsxxxx)

Microarray/:
-- All Variants file to create CombinedKit from BAM; one for each build 
     and naming style
-- Microarray RAW file templates for headers and bodies to target 
     generating microarray files
-- Ploidy definition file