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msesia / knockoffgwas

A flexible tool for the multi-resolution localization of causal variants across the genome, accounting for population structure.
https://msesia.github.io/knockoffgwas
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How many IBD segments is too many? #3

Closed biona001 closed 2 years ago

biona001 commented 2 years ago

Hello,

I simulated 2k samples and 50k SNPs, for which RaPID returned around 6000 IBD segments. On this data, snpknock2 seems basically stuck at Generating related knockoffs (waited ~30 min and the progress bar did not move at all). After decreasing IBD segments to 20, the knockoffs were generated in ~20 min or so.

msesia commented 2 years ago

The number of IBD segments isn't a bottleneck in itself, the problem may be that the "IBD-related families" (that's what they're called in the paper) are too large. What I mean is that if you look at the relatedness graph for your haplotype sequences, where two nodes are connected if they share an IBD segment, it may be that the connected components are too large. The complexity of the algorithm depends on the size of the connected components. If it makes sense with your data, try to make the connected components smaller. In the paper, we only considered IBD segments between individuals with self-reported relatedness, and excluding a handful of individuals, so that the largest IBD-sharing family wouldn't be too large.

The entire software is multi-threaded, not just reading the BGEN data.

From: Benjamin Chu @.> Sent: Wednesday, October 27, 2021 4:17 PM To: msesia/knockoffgwas @.> Cc: Subscribed @.***> Subject: [msesia/knockoffgwas] How many IBD segments is too many? (Issue #3)

Hello,

I simulated 2k samples and 50k SNPs, for which RaPID returned around 6000 IBD segments. On this data, snpknock2 seems basically stuck at Generating related knockoffs (waited ~30 min and the progress bar did not move at all). After decreasing IBD segments to 20, the knockoffs were generated in ~20 min or so.

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biona001 commented 2 years ago

Thank you for the prompt response! That makes a lot of sense.