Preposed changes for GRCh38

Preposed changes for GRCh38.md

#Preposed changes for GRCh38

Reference/ 
	GRCh37/
	GRCh38/

GATK_Bundle
	GRCh37/
	GRCh38/

* All Region files are built from refseq(37/38) GFF3 CDS regions
Regions/
	GRCh37/
		UCGD.CDS.Region.bed (alignstats & VQSR) 
		UCGD.WGS.Region.bed (alignstats & VQSR) 
		WGS/chr*bed (VEP & GVCFTyper)
	GRCh38/
		UCGD.CDS.Region.bed (alignstats & VQSR) 
		UCGD.WGS.Region.bed (alignstats & VQSR) 
		WGS/chr*bed (VEP & GVCFTyper)
		
* Backgrounds
1000G/
	GRCh37/
		*g.vcf.gz (soft-linked list of GVCFs to use from each population..) GBR/ CEU/ FIN/ ..
	GRCh38/
		*g.vcf.gz (soft-linked list of GVCFs to use from each population..) GBR/ CEU/ FIN/ ...

UCGDBackgrounds/
	GRCh37/
		*g.vcf.gz (soft-linked list of GVCFs to use from each population..)
		*g.vcf.gz (soft-linked list of Longevity + CEPH Grandparents) <--- this will go away when dynamic background is put into place.
	GRCh38/
		*g.vcf.gz (soft-linked list of GVCFs to use from each population..)
		*g.vcf.gz (soft-linked list of Longevity + CEPH Grandparents) <--- this will go away when dynamic background is put into place.
	

Preposed changes to the Processing Directory structure:

UCGD/
Primary_Data/ <--- ln -s
	GRCh37/
	├── Analysis
	├── Data
	│ ├── PolishedBams 
	│ └── Primary_Data <----------- remove?
	├── Project_Setup 
	├── Reports
	│ ├── alignstats
	│ ├── fastp
	│ ├── flagstat
	│ ├── goleft
	│ ├── peddy
	│ ├── RunLogs
	│ ├── stats
	│ └── vep
	└── VCF
		├── Complete
		└── GVCFs

	GRCh38/
	├── Analysis
	├── Data
	│ ├── PolishedBams 
	│ └── Primary_Data 
	├── Project_Setup 
	├── Reports
	│ ├── alignstats
	│ ├── fastp
	│ ├── flagstat
	│ ├── goleft
	│ ├── peddy
	│ ├── RunLogs
	│ ├── stats
	│ └── vep
	└── VCF
		├── Complete
		└── GVCFs