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scarus's Introduction

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Scarus

Scarus (Simple Code for ACMG Rule Utilisation and Scrutiny) is a software package for the autoamted evaluation of ACMG criteria for structural variants.

Also, here are some facts on Scarus/Parrotfish:

#1

Scarus is a genus of parrotfishes.

[...]

Plutarch had written that scarus fish "swim together in shoals and ingeniously and heroically free each other when caught in a net." The scarus thus "denoted reciprocal assistance in the fight for survival."

-- "Scarus" -- Wikipedia

#2

Their feeding activity is important for the production and distribution of coral sands in the reef biome, and can prevent algal overgrowth of the reef structure. The teeth grow continuously, replacing material worn away by feeding

-- "Parrotfish" -- Wikipedia

#3

Corallivores are an important group of reef organism because they can influence coral abundance, distribution, and community structure.

-- "Corallivore" -- Wikipedia

Developer Documentation

The contents of this section are only relevant to developers of Scarus itself.

Managing Project with Terraform

# export GITHUB_OWNER=bihealth
# export GITHUB_TOKEN=ghp_TOKEN

# cd utils/terraform
# terraform init
# terraform import github_repository.scarus scarus
# terraform validate
# terraform fmt
# terraform plan
# terraform apply

scarus's People

Contributors

holtgrewe avatar dependabot[bot] avatar

Watchers

avatar Oliver Stolpe avatar avatar avatar Jethro Rainford avatar

scarus's Issues

Initial implementation of DUP / copy number gain sections

Is your feature request related to a problem? Please describe.
We do not have any implementation of ACMG rules for copy number gain / DUP.

Describe the solution you'd like
Implement the rules.

Describe alternatives you've considered
N/A

Additional context

Properly implement PVS1 rule set.

Is your feature request related to a problem? Please describe.
Currently, we have not implemented the Abou Tayoun et al. (2018) rule set yet.

Describe the solution you'd like
Implement this rule set.

Describe alternatives you've considered
N/A

Additional context
N/A

Refine meaning of "genomic material"

Is your feature request related to a problem? Please describe.
Our interpretation of DEL was "any sequence" so far, but reading the DUP rules, this appears wrong. What is meant is here functional content, such as regulatory elements and genes.

Describe the solution you'd like
Review this interpretation and adjust rules.

Describe alternatives you've considered
N/A

Additional context
N/A

Integrate population / polymorphism databases

Is your feature request related to a problem? Please describe.
We should integrate databases of known population / tentative benign CNVs.

Describe the solution you'd like
Add gnomAD-SV and gnomAD/ExAC-CNV

Describe alternatives you've considered
N/A

Additional context
N/A

Use snake_case for serialization everywhere

Is your feature request related to a problem? Please describe.
We should use snake_case for serialization, in particular for the result enums.

Describe the solution you'd like
N/A

Describe alternatives you've considered
N/A

Additional context
N/A

Implement command line interface

Is your feature request related to a problem? Please describe.
We currently have no way of obtaining a prediction from Scarus.

Describe the solution you'd like
Implement a command line interface that allows to score individual variants.

Describe alternatives you've considered
N/A

Additional context
N/A

Implement regulatory elements

Is your feature request related to a problem? Please describe.
We currently do not consider regulatory elements by #1 and #2. We really should.

Describe the solution you'd like
Incorporate regulatory elements in DEL & DUP rules.

  • provide regulatory element data
  • implement in DEL
  • implement in DUP

Describe alternatives you've considered
N/A

Additional context
N/A

Integrate disease gene annotation

Is your feature request related to a problem? Please describe.
We currently do not annotate whether a reported overlapping gene is a disease gene.

Describe the solution you'd like
Annotate genes whether they are known OMIM disease genes.

Describe alternatives you've considered
N/A

Additional context
N/A

Clarify meaning of "genomic content" for ClinVar/Population SV evaluation

Is your feature request related to a problem? Please describe.
For overlapping SVs from ClinVar and gnomAD we currently use the reciprocal overlap criteria. This appears somewhat insufficient as genomic content is more relevant.

Describe the solution you'd like
Re-evaluate the rules.

Describe alternatives you've considered
N/A

Additional context
N/A

Initial implementation of DEL / copy number loss sections

Is your feature request related to a problem? Please describe.
We do not have any implementation of ACMG rules for copy number loss / DEL.

Describe the solution you'd like
Implement the rules.

Describe alternatives you've considered
N/A

Additional context

Make established variants known to 2D-2/2D-3 rule.

Is your feature request related to a problem? Please describe.
We currently don't have established variants yet in rules 2D-2 and 2D-3.

Describe the solution you'd like
Use annonars ClinVar variants here.

Describe alternatives you've considered
N/A

Additional context

Implement web server interface

Is your feature request related to a problem? Please describe.
While a command line interface (#29) is useful, we eventually need to run a web server.

Describe the solution you'd like
Implement actix-based web server as we have done in annonars, viguno, etc.

Describe alternatives you've considered
N/A

Additional context
N/A

Provide ClinVar SVs for rules sections 4.

Is your feature request related to a problem? Please describe.
We currently don't have any ClinVar variants in scarus yet but they are needed for Section 4.

Describe the solution you'd like
Provide ClinVar SVs and integrate with Section 4.

Describe alternatives you've considered
N/A

Additional context

Use "once" fixtures in tests

Is your feature request related to a problem? Please describe.
We currently use fixtures but don't mark them as once. This is flow.

Describe the solution you'd like
Make the fixtures once.

Describe alternatives you've considered
N/A

Additional context
N/A

Integrate PVS1 with rules 2E of DEL/DUP

Is your feature request related to a problem? Please describe.
For the time being, we have not implemented the full PVS1 rule set in 2E (#1, #2).

Describe the solution you'd like
After #5, implement with rules 2E of DEL/DUP.

Describe alternatives you've considered
N/A

Additional context

Use data from annonars

Is your feature request related to a problem? Please describe.
For some data that is available in annonars, we still have our local information. We should obtain all data from other libraries such as annonars, ...

Describe the solution you'd like
The following should come from annonars:

  • clingen dosage genes
  • clingen dosage regions
  • DECIPHER HI predictions
  • gnomAD gene constraints

Describe alternatives you've considered
N/A

Additional context
N/A

Only report single gene / region where applicable

Is your feature request related to a problem? Please describe.
In a number of places we return Vecs of regions/genes. In some it does not make sense.

Describe the solution you'd like
Review these data structures in the result modules and trim this down.

Describe alternatives you've considered
N/A

Additional context
N/A

Implement haploinsufficiency / triplosensitivity scores

Is your feature request related to a problem? Please describe.
We currently only use ClinGen annotations of regions and genes. We should extend this to less established genes.

Describe the solution you'd like
Incorporate the pHet/pTriplo scores that also are available in Decipher.

Describe alternatives you've considered
N/A

Additional context
N/A

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