Feature request for "shapeit -convert --input-graph --output-sample" ?

odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool

MIT License

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Feature request for "shapeit -convert --input-graph --output-sample" ? #35

Open pauline-ng opened 3 years ago

pauline-ng commented 3 years ago

Dear Prof. Delaneau,

In an older version of shapeit, there was an option to sample a pair of haplotypes with: shapeit -convert --input-graph chr20.graph --output-sample gwas.phased

I see shapeit4 outputs a graph, but currently I see no options for "input-graph" or "output-sample". I was wondering if there were plans to implement that?

(I can't use shapeit2 because I'm using phasing options in shapeit4 not available in shapeit2, so the graph won't be the same).

Best, Pauline

odelaneau commented 3 years ago

I recently implemented this. It's located in tools/bingraphsample. It's still under development. If you need some help to run it, email me directly.

Best,