Feature/grch38 #904
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Feature/grch38 #904
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- Added chr prefix for 2 recipe regexp looking for miochondrial contig
- Added download from gatk google bucket for human genome build
- Modified system call to use IPC::Cmd instead of open3 due to cache issue - Adjusted hg38 to grch38 for test data - Added download from gatk google bucket for human assembly - Added download of recent grch38 clinvar vcf
- Added primary assembly contigs per version to constants - Refactored set_contigs sub to use constant and set alt_loci to file_info
contigs - Added test
- Gatk baserecal (mills and 100g indels) - Gnomad v r2.1.1 - Fixed test broken by hg38 -> grch38
- Added optional parameter to specify call regions file to MIP rd_dna - Added use in recipe and program - Added download from reference dir on github
- Added synonyms option to vep program API - Added utility sub to get synonyms file depending on genome build version in recipes - Updated test - Added test
- Increased memory for sv_annotate from 7 to 19 Gb since vcfanno ran out of memory
jemten
reviewed
Aug 14, 2019
lib/MIP/Recipes/Analysis/Vep.pm
Outdated
| @@ -1562,6 +1597,60 @@ sub _get_assembly_name { | |||
| return $assembly_version; | |||
| } | |||
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| sub _get_vep_synonyms_file { | |||
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Is this sub needed? Can't you just use the create_vep_synonyms_file sub directly. It looks like that sub should return directly if it can't find a vep synonym hash, which should only be present for grch38
Co-Authored-By: Anders Jemt <jemten@users.noreply.github.com>
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