Closed koido closed 1 year ago
Hi Masuru,
I think ligate and phase_rare are safe, there's no random sampling in there. Multi-threading and reproducibility should be possible.
But as you mention; this is not the case for phase_common.
Cheers;
Olivier Delaneau
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Le ven. 21 avr. 2023 à 06:13, Masaru Koido @.***> a écrit :
Hi,
Thanks for developing such an excellent tool.
I noticed that if I want to make the phase_common results reproducible, I have to use a single thread (and keep the seed, although the default seed is fixed). This was described in the SHAPEIT4's document as follows:
- Reproducibility Making reproducible runs can sometimes be useful. To do so, you need to specify the random generator seed using --seed and to use a single thread. Using multi-threading prevents reproducibility.
Regarding ligate and phase_rare, should I use a single thread to make it reproducible?
Although I want to use multiple threads to speed up, I am also concerned about reproducibility and its potential effects on my downstream analysis.
Best,
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Hi Olivier,
Thank you very much for your helpful response.
Best, Masaru
Hi,
Thanks for developing such an excellent tool.
I noticed that if I want to make the
phase_common
results reproducible, I have to use a single thread (and keep the seed, although the default seed is fixed). This was described in the SHAPEIT4's document as follows:Regarding
ligate
andphase_rare
, should I use a single thread to make it reproducible?Although I want to use multiple threads to speed up, I am also concerned about reproducibility and its potential effects on my downstream analysis.
Best,