tool requests - Githubissues

joellepasman commented 3 years ago

Tools that could be added to the containers:

MAGMA https://ctg.cncr.nl/software/magma
Rpackage Genomic SEM https://github.com/GenomicSEM/GenomicSEM
Rpackage Two Sample Mendelian Randomization https://mrcieu.github.io/TwoSampleMR/
Rpackage gsmr (+ dependencies and secondary tools)

joellepasman commented 3 years ago

Also, maybe we should discuss if we want to use PRSice for all our PRS work. For example, we could implement LDpred, GCTA-SBLIP or SBayesR, which have shown greater power and accuracy.

ofrei commented 3 years ago

@joellepasman Noted, I'll look into this - thank you!

For PRS computation, I think we can start with PRSice2 because it's basic and very simple, but indeed it's good to have other software on your list available. Could you please include the download links or documentation for LDpred, GCTA-SBLIP and SBayesR tools? I'm aware of these tools, just want to double-check (e.g. SBayesR is probably part of the GCTB package which I'm partly confusing with GCTA ).

joellepasman commented 3 years ago

GSMR: https://cnsgenomics.com/software/gsmr/ LDpred: https://github.com/bvilhjal/ldpred GCTA-SBLUP: https://cnsgenomics.com/software/gcta/#SBLUP SBayesR: https://cnsgenomics.com/software/gctb/#Tutorial

ofrei commented 3 years ago

MAGMA was added to gwas.sif
GenomicSEM, TwoSampleMR, and GSMR tools were added to r.sif
LDpred was added to python3.sif
GCTA-SBLUP and SBayesR are part of GCTA and GCBT tools which are already available in gwas.sif.
prsice2 is already part of gwas.sif

For the MAGMA, I've included the official MAGMA reference data in $COMORMENT/containers/reference/magma. Then one should simply follow official MAGMA tutorial, https://ctg.cncr.nl/software/magma .

For GCTA and GCTB I wasn't sure what test data should be included - please let me know if there are some demo datasets needed to follow https://cnsgenomics.com/software/gctb/#Tutorial or https://cnsgenomics.com/software/gcta/#SBLUP, it would be good to include those dataset in https://github.com/comorment/containers/tree/main/reference/examples

I haven't tested GenoicSEM and TwoSampleMR packages - please let me know if you have a chance to try the out and they don't work.

For GSMR, the demo data is available in $COMORMENT/containers/reference/example/gsmr , and one could follow https://cnsgenomics.com/software/gsmr/ tutorial (see some notes here ).

For LD pred, I've tested that its unit tests work well (ldpred-inttest) and ldpred --help works, but I haven't made a use case.

Close for now, please reopen if any of the tools have problems

joellepasman commented 3 years ago

Here are the tutorial data for GCTB (I don't think there is a tutorial for SBLUP): https://cnsgenomics.com/software/gctb/#Download

Some additional tools that would be good to include (I definitely want to use HDL):

Latent causal variable model: https://github.com/lukejoconnor/LCV High-Definition Likelihood for genetic correlation: https://github.com/zhenin/HDL S-PrediXcan: https://github.com/hakyimlab/MetaXcan

We might also want to use within-family MR but I think that's not a separate package or if there's even an established way of doing it, do you have thoughts about that?

comorment / containers

tool requests #8