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Diffstat (limited to 'topics/data/precompute/steps.gmi')
| -rw-r--r-- | topics/data/precompute/steps.gmi | 32 |
1 files changed, 29 insertions, 3 deletions
diff --git a/topics/data/precompute/steps.gmi b/topics/data/precompute/steps.gmi index 33915cd..75e3bfd 100644 --- a/topics/data/precompute/steps.gmi +++ b/topics/data/precompute/steps.gmi @@ -8,12 +8,12 @@ We will track precompute steps here. We will have: * [X] steps g: genotype archives (first we only do BXD-latest, include BXD.json) * [X] steps k: kinship archives (first we only do BXD-latest) -* [ ] steps p: trait archives (first we do p1-3) +* [X] steps p: trait archives (first we do p1-3) Trait archives will have steps for -* [+] step p1: list-traits-to-compute -* [ ] step p2: gemma-lmm9-loco-output: Compute standard GEMMA lmm9 LOCO vector with gemma-wrapper +* [X] step p1: list-traits-to-compute +* [+] step p2: gemma-lmm9-loco-output: Compute standard GEMMA lmm9 LOCO vector with gemma-wrapper * [ ] step p3: gemma-to-lmdb: create a clean vector The DB itself can be updated from these @@ -74,3 +74,29 @@ Note that it (potentially) includes the parents. Also the strain-id is a string from guile-hashing and guile-gcrypt modules. In the next step we have to check the normal distribution of the trait values and maybe winsorize outliers. +Actually we should brute force the default first. +Be interesting to see the effect of handling outliers and normalisation of phenotypes. + +# Step p2: run GEMMA lmm9 + LOCO + +Last week I checked out Arun's CCWL. Anything more complicated that a few steps can go into CCWL. It will also handle cluster work loads using, for example, toil. We will use trait files + genotypes as inputs for gemma-wrapper initially. + +p1: Workflow 1: + +``` +batch traits from DB +``` + +p2+p3: Workflow 2: + +``` +batched traits, genotypes -> + gemma-wrapper -> + lmdb'ize +``` + +p4: Workflow 3: + +``` +Update DB +``` |