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brentp / somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
MIT License
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somalier ancestry : Argument list too long #81

Closed nrosewick closed 2 years ago

nrosewick commented 2 years ago

Related to https://github.com/brentp/somalier/issues/37

I tried somalier ancestry on ~50k samples but I got a "Argument list too long" error. Any idea how to fix it ? or maybe provide a txt file with list of somalier files in input ?

Thank you N.

brentp commented 2 years ago

Hi, you can use a glob (and quote it to prevent it from being expanded by your shell), something like:

somalier ancestry ... '/path/to/my-samples/*/*.somalier' ++ '/path/to/1kg/*.somalier'
nrosewick commented 2 years ago

Ok great. It's working perfectly :-)

Thanks Brent !

brentp commented 2 years ago

Great. Thanks for following up. I should update the docs, but be careful with the somalier ancestry results. I'd call it "still in development". It doesn't do well for unknown ancestries. It will confidently predict an ancestry even if it should be uknown or low confidence, but should work quite well for ancestries matching those in your training set (or 1kg if that's what you're using).