Allow conditioning on a variant

[statgen]

Allow conditioning on a variant

[dtaliun]

Hi Peter, I have also a pythonic code that uses raw tabix’ed VCFs + numpy linear algebra (which can be speeded up compiling against BLAST/LAPACK). Daniel

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On Feb 23, 2017, at 5:26 PM, Peter VandeHaar ***@***.***> wrote: Goncalo says that all you need is r between that variant and each other for your data. (separate for cases and controls?) Option 1: (I GUESS SO) Set up an LD server that references the raw data, probably by copying Daniel's HVCF. Option 2: (NAH) Pre-compute r for all variant pairs within 300kb from the raw data. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#45>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMPXBGoFrmcvehCMquL90xJ_wEbL0QtPks5rfgeAgaJpZM4MKlN6>.

[pjvandehaar]

If some 300kb regions have 10x the average variant density, that could somewhat increase the size of pre-computed correlations. If some have 100x the average (ie, 1% of all variants in 0.01% of the genome), we'll have a problem. Oh well, hopefully that doesn't happen.

Maybe we should only allow conditioning on variants with pval < 1e-4. But if we want to support conditional meta-analysis, then we can't have a restriction like that.

How many variants will there probably be in TOPMed?

[abecasis]

Most variants and regions will be 10^-4 for something. Densest regions are around HLA genes and MHC on chromosome 6. If we set this up right, we should only need one covariance table for many traits and variants in one PheWeb. G

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Sent from my iPhone

On Mar 6, 2017, at 2:45 PM, Peter VandeHaar ***@***.***> wrote: If some 300kb regions have 10x the average variant density, that could somewhat increase the size of pre-computed correlations. If some have 100x the average (ie, 1% of all variants in 0.01% of the genome), we'll have a problem. Oh well, hopefully that doesn't happen. Maybe we should only allow conditioning on variants with pval < 1e-4. But if we allow conditional meta-analysis, then we can't have a restriction like that. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[pjvandehaar]

(While I'm doing this, remember to also use study-specific LD for showing LD in LZ. I'm not sure how we'll handle meta-analysis LD. Perhaps it'd be fun to toggle 1000G vs study-specific LD, &c?)