Removing MuTect1#567
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szilvajuhos
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szilvajuhos
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We have to make a new version for this (2.1, as it is not a bugfix).
Seems Mutect2 is still present at multiple locations in the germline code, could you please double-check those? We can actually keep FreeBayes as many people are using it for germline.
| file("*.vcf.gz.tbi") into vcfConcatenatedTbi | ||
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| when: ( 'haplotypecaller' in tools || 'mutect1' in tools || 'mutect2' in tools || 'freebayes' in tools ) && !params.onlyQC | ||
| when: 'haplotypecaller' in tools && !params.onlyQC |
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I am a bit confused here, so it is germline calling, so all the somatic callers are removed, if I am correct.
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I remember now, germlineVC.nf definitively needs more cleaning.
Do you want me to do that in this PR, or in a separate one?
Like in the one that will fix the BQSR thingy
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Would be nice to keep it in a single PR (so we can backout :) ) There is no rush, we are going to use v2.0.0 for few weeks anyway.
| 'gvcf-hc' : "${params.outDir}/VariantCalling/HaplotypeCallerGVCF", | ||
| 'manta' : "${params.outDir}/VariantCalling/Manta", | ||
| 'mutect1' : "${params.outDir}/VariantCalling/MuTect1", | ||
| 'mutect2' : "${params.outDir}/VariantCalling/MuTect2", |
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So Mutect2 also can be removed.
| @@ -679,7 +659,6 @@ def defineToolList() { | |||
| 'freebayes', | |||
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ditto freebayes though that can be used for germline, so, if somebody wants to have that, s/he can still use it.
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Can we use Freebayes for germline?
We're not doing that yet.
Which settings should we use?
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Aaa, you are right, just remove it.
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