Updated notes and details for release

Author: PedalheadPHX

grch38_hg38_ucsc_contigs/README.md

@@ -1,11 +1,34 @@
-This folder contains resource files and templates to support Homo sapiens GRCh38 reference genome build using UCSC style contig names
+### Version Notes
+This folder contains resource files and templates to support Homo sapiens GRCh38 reference genome build using UCSC style contig names.
+
+* The database and position files DO NOT have identical contig names
+    * positions file (positions_387_hg38_ucsc.txt)
+        * contig names match the reference genome fasta contig names with "chr" prefixing the primary chromosome contigs
+    * database file (databaseV5_hg38_ucsc.ini)
+        * contig names DO NOT include "chr" prefix
+        * This is because the -add option seems to require that the contig names are single character strings.  To support this limitation the "geno" script produces a VCF without chr contig names even though the input targets file and input BAM have contigs with the "chr" prefix
+
+### Changes
+* Genotyping is now executed by bcftools 1.0 or later.  Removing the previous limitation that genotyping need to be done with older samtools (v0.19) mpileup and bcftools.
 
-It also supports the usage of updated variant calling using samtools v1.9 or later
 
 ### Issues
 * The lift-over of the defined 387 variants failed for one variant
     * Partially deleted in new:
         * chr1:206760685-206760686
 * Because the database MUST be 387 variants we need to add one additional variant
-    * Added the following for testing (May Update):
-        * chr22 32491163
+    * Added the following for testing (Might Update in future):
+        * chr22 32491163
+        
+### Requirements (available in user $PATH)
+* java
+* bcftools v1.0 or later
+
+### Tested Enviroment
+* java
+    * openjdk version "1.8.0_141"
+    * OpenJDK Runtime Environment (build 1.8.0_141-b16)
+    * OpenJDK 64-Bit Server VM (build 25.141-b16, mixed mode)
+* bcftools
+    * Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
+    * Version: 1.9 (using htslib 1.9)