From 0e36aba6c4325da5dec9d466d9be4b04c0ead35c Mon Sep 17 00:00:00 2001 From: PedalheadPHX Date: Thu, 14 Mar 2019 14:55:44 -0700 Subject: [PATCH] Updated notes and details for release --- grch38_hg38_ucsc_contigs/README.md | 31 ++++++++++++++++++++++++++---- 1 file changed, 27 insertions(+), 4 deletions(-) diff --git a/grch38_hg38_ucsc_contigs/README.md b/grch38_hg38_ucsc_contigs/README.md index 1135189..654d51d 100644 --- a/grch38_hg38_ucsc_contigs/README.md +++ b/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 \ No newline at end of file + * 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) \ No newline at end of file