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 ;-) bioconda/bioconda-recipes#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