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| 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. | ||
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| * 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 | ||
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| ### 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. | ||
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| It also supports the usage of updated variant calling using samtools v1.9 or later | ||
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| ### 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 | ||
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| ### Requirements (available in user $PATH) | ||
| * java | ||
| * bcftools v1.0 or later | ||
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| ### 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) |