update StrainID with hg38 db and scripts

Add support for hg38 and expanded cell lines on StrainID

-add hg38_VCF db with similar cell lines to hg19_VCF
-add hg38_ENCODE db with ENCODE cell lines at least 250 variants big
-add scripts and refs for building full hg38_DepMap db
-update README to describe how Model.csv was downloaded.
-minor fix to generate_sacCer3_VariantDB.sh usage typo
-.gitignore updated appropriately

Author: owlang

.gitignore

@@ -2,3 +2,10 @@
 EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.*
 EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa*
 EpitopeID/hg19_EpiID/FASTA_genome/genome.fa*
+StrainID/hg38_VCF
+StrainID/hg38_ENCODE
+StrainID/hg38_DepMap
+StrainID/utility_scripts/header.vcf
+StrainID/utility_scripts/CL_names.txt
+StrainID/utility_scripts/CSV
+StrainID/utility_scripts/hg38_DepMap

StrainID/hg38_ENCODE.tar.gz

@@ -0,0 +1,10 @@
+
+### Model.csv
+Downloaded from https://depmap.org/portal/download/all/?releasename=DepMap+Public+23Q2&filename=Model.csv on May 14, 2023
+
+
+### generate_hg38_VariantDB.sh
+Download all DepMap (Broad) variants based on `Model.csv` accessions and cell line names.
+
+### generate_sacCer3_VariantDB.sh
+Download all Song et al (2015) variants and perform BedTools intersect for unique substitutions (better uniquely characterize strain) and format into VCF files for StrainID.

StrainID/hg38_VCF.tar.gz

@@ -18,7 +18,7 @@
 usage()
 {
     echo 'generate_sacCer3_VariantDB.sh'
-    echo 'eg: bash generate_sacCer3_GenomeAnnotation.sh'
+    echo 'eg: bash generate_sacCer3_VariantDB.sh'
     exit
 }