Running SnpEff and VEP at once, also fixing CLI for annotators#555
Running SnpEff and VEP at once, also fixing CLI for annotators#555maxulysse merged 11 commits intoSciLifeLab:masterfrom szilvajuhos:master
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Seems safe enough, I approve
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| def defineStepList() { | ||
| return [ | ||
| 'annotate' |
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We don't need this defineStepList function anymore.
Only one step is available at this point.
| 'bcftoolsStats' : 'Reports/BCFToolsStats', | ||
| 'snpeff' : 'Annotation/SnpEff', | ||
| 'vep' : 'Annotation/VEP', | ||
| 'merge' : 'Annotation/merged' |
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I believe that there is a merging error here.
The definition of the directory map happens once here, and once in the defineStepList.
| 'snpeff', | ||
| 'vep' | ||
| 'vep', | ||
| 'merge' |
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I prefer lists to be sorted, but that's not really important here ;-)
| chrY 1268800 1310381 CSF2RA | ||
| chrY 1462572 1537107 P2RY8 | ||
| chrY 2691179 2741309 CD99 | ||
| chr1 1785285 1891117 GNB1 |
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Why do we have so many changes in this file?
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Long story short: it is a quasi-panel, ever-expanding list of genes related to cancers.
| // we have to exchange the channels | ||
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| if('merge' in tools) { | ||
| vcfForVep = snpEffOutputVCFs |
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So if I want to have snpEFF, VEP and merged VCF it's not possible?
Can't we use that?
vcfForVep = vcfForVep.mix(snpEffOutputVCFs)
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That will be a new feature if it is going to be needed at all. Testing takes time and I do not want to add stuff that is never going to be used or relatively easy to do with some scripting.
maxulysse
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Running SnpEff an VEP at once, also fixing CLI for annotators
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Resolving #547