Community feedback needed: Consider other tools

[maxulysse]

Issue by @maxulysse, moved from SciLifeLab#666

• 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
• TrackSig to infer mutational signatures in cancer over time
• DriverPower to discover potential coding and non-coding cancer driver elements from tumour whole-genome or whole-exome somatic mutations
• SVclone for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data
• 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
• Google DeepVariant Deep neural network to call genetic variants from next-generation DNA sequencing data
• Octopus
• mosdepth fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
• rock circos plot out of manta
• DeepTrio
• SmuRF for Random Forest Ensembl Somatic Calling
• PureCN for estimating purity/ploidy
• Lofreq a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. LoFreq is very sensitive; most notably, it is able to predict variants below the average base-call quality (i.e. sequencing error rate).
• DeepSomatic extension of deep learning-based variant caller DeepVariant
• MEDICC2 Minimum Event Distance for Intra-tumour Copy-number Comparisons
• DPClust Dirichlet Process based methods for subclonal reconstruction of tumours
• LINX annotation, interpretation and visualisation tool for structural variants
• FindDNAFusion a combinatorial pipeline for the detection of cancer-associated gene fusions in next-generation DNA sequencing data

[davidmasp]

Would something like somalier be interesting? just saw in twitter that now it can be integrated in MultiQC. I am not sure if there is a conda package though...

[maxulysse]

Nothing yet in Bioconda.
What would be your use case with somalier?

[davidmasp]

Maybe not superuseful in terms of new features. I understand it identifies that tumor/ normal come from the same patient. I think it could be useful in some set ups and maybe also somatic calling for cell lines for instance which aren’t exactly a classical use case for a somatic vc pipeline. Indeed idk about the tool much though.

[mvelinder]

I'd throw my support in for DeepVariant integration under --tools

Is that still a priority? It seemed like it was being worked on back in #105

Thanks!

[mvelinder]

ExpansionHunter would also be a great addition under --tools

[maxulysse]

Hi @mvelinder both are tools that we indeed considered.
At the time of #105 deepvariant seemed to big to be integrated into sarek.
with DSL2, it would make sense to have it within sarek, so we currently have plan to have all the necessary modules made in nf-core/modules and then integrate into sarek.

[egenomics]

Hi,

For clinical environments it would be great to have a depth calculation tool. Mosdepth is a winner, as already suggested.

Another important tool would be a cnv caller. Manta is not a good tool for it, at least for gene panels. An easy and validated solution would be Exomedepth:
https://pubmed.ncbi.nlm.nih.gov/32561899/

[abhi18av]

I'd like to suggest addition of DeepTrio which builds upon DeepVariant, aimed at variant calling of trios or duos.

[FriederikeHanssen]

Expansionhunter & HSMetrics have both been suggested by @marchoeppner https://nfcore.slack.com/archives/CGFUX04HZ/p1647518666493429?thread_ts=1647517444.673109&cid=CGFUX04HZ something for 3.1?

[gorgitko]

Hi, deepvariant has been already incorporated, but without deepTrio, right?