Consider other tools

[maxulysse]

EDIT with a checklist of tools

• [ ] ExpansionHunter for estimating repeat sizes
• [ ] QDNAseq CNVs for shallow WGS
• [ ] CNVkit for CNVs
• [ ] deconstructSigs for mutational signatures
• [ ] ditto mutation-signatures
• [ ] SomaticSeq ensemble caller and machine learning
• [ ] MSIsensor for replication slippage variants at microsatellite regions
• [ ] Oncotator for annotating human point mutations and indels
• [ ] MutSig for Mutation Significance checks
• [ ] HsMetrics better QC
• [ ] CNNScoreVariants Annotate a VCF with scores from a Convolutional Neural Network (CNN).
• [ ] SignatureAnalyzer yet an other mutation signature analyser from Broad
• [ ] PROSIC2 is a caller for somatic variants in tumor-normal sample pairs
• [ ] seqCAT Evaluation of SNV profiles
• [ ] varlociraptor A Rust library for variant calling using a latent variable model
• [ ] GATK CNN Convolutional Neural Net to filter annotated variants

[maxulysse]

Latest version available on bioconda is 2.0.8. Latest version is 2.5.5, so it would good to update the recipe on bioconda to facilitate the use of this tool

[apeltzer]

You're welcome ;-) https://github.com/bioconda/bioconda-recipes/pull/11386

[apeltzer]

To be fair: That one was super easy ;-)

[maxulysse]

I'm impressed it was that easy. Thanks a lot.

[szilvajuhos]

The checklist for all the others we should check:

• [ ] ExpansionHunter for estimating repeat sizes
• [ ] QDNAseq CNVs for shallow WGS
• [ ] CNVkit for CNVs
• [ ] deconstructSigs for mutational signatures
• [ ] ditto mutation-signatures
• [ ] SomaticSeq ensemble caller and machine learning
• [ ] MSIsensor for replication slippage variants at microsatellite regions
• [ ] Oncotator for annotating human point mutations and indels
• [ ] MutSig for Mutation Significance checks
• [ ] HsMetrics better QC
• [ ] CNNScoreVariants Annotate a VCF with scores from a Convolutional Neural Network (CNN).
• [ ] SignatureAnalyzer yet an other mutation signature analyser from Broad
• [ ] PROSIC2 is a caller for somatic variants in tumor-normal sample pairs
• [ ] seqCAT Evaluation of SNV profiles

[maxulysse]

Transferred to the new nf-core/sarek repo