Annotation with or without cache #719
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| ## Downloading cache | ||
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| An helper script has been designed to help downloading snpEff and VEP cache. |
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You could add here as well that this is only necessary if one is not running on uppmax and do not wish to use the specific containers.
| @@ -12,6 +13,8 @@ Subsets of all containers can be downloaded: | |||
| - For annotation for GRCh38, you will need: | |||
| - [snpeffgrch38](#snpeffgrch38-) | |||
| - [vepgrch38](#vepgrch38-) | |||
| - For annotation with cache use: | |||
| - [sarek](#sarek-) | |||
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But in that case, I could probably say, you should already have this one...
| @@ -112,6 +111,23 @@ Possible values are: | |||
| Choose vcf to annotate. | |||
| Different vcfs to be separated by commas. | |||
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| ### --annotate_cache | |||
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Could you clarify the edge cases, for example: using: --annotate_cache but not either --snpEff_cache or --vep_cache; using --snpEff_cache without --annotate_cache?
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won't work.
You need to use --annotate_cache with --snpEff_cache or/and --vep_cache
If you use only --annotate_cache it's not using cache
If you use only --snpEff_cache or/and --vep_cache it's not using cache either
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Yes, can you have that in the docs? It will not crash though, it will just not do what one thinks it does. Right?
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OK, I will specify all that then
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Currently seems to be working well on |
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Annotation worked well on munin, with and without the annotation cache. |
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also closes #554 |
--annotation_cacheparameter to use the annotation cache, which need to be used with:---snpEff_cacheto specify snpEff cache--vep_cacheto specify VEP cachePR checklist
devbranch./scripts/test.sh -p docker -t ALL).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedEDIT: Forgot the details...