User: curious
curious • 470
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Posts by curious
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... Lets say I have (dumb example)
CHROM POS REF ALT
1 1 A T
Say this site is hg19 and Ref allele is referring the forward strand and maps to position 100 on hg38.
You can just blindly update the position like this correct?
CHROM POS REF ALT
1 100 A ...
written 12 days ago by
curious • 470
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... I have a bim file that has lines like this
`6 rs563372567 0 33966734 * G`
does this just mean "not G" at a multiallelic site? Or a single nucleotide deletion perhaps (in this case deletion of G)? ...
written 12 days ago by
curious • 470
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... That would make too much sense :) ...
written 6 weeks ago by
curious • 470
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... This is not homework its just an example I found online.
They are testing association between HLA alleles and some binary disease [here][1]
in the data frame they have col `DQDRa1` and `DQDRa2` for haplotypes of HLA gene DQDR. It can be 10 different alleles which they recode into a number of dumm ...
written 6 weeks ago by
curious • 470
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... It was just a dummy example to illustrate the idea. I was thinking more about biobanking where you cant just pay for more cases ...
written 8 weeks ago by
curious • 470
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... To expand on this, how would it look if you did have covariate (sex). For example say I have a multialleleic locus with three possible snps:
data <- data.frame("snp1"=c(runif(n=150, min=0,max=2),
c(runif(n=50, min=0,max=2))),
"snp2"=c(runi ...
written 8 weeks ago by
curious • 470
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... Lets say you had 100,000 samples, but were looking at some super rare diseases. At some point I would think even given the huge overall sample size that the number of cases makes interpretation hard, even if some really small p values are obtained via GWAS.
is 5 cases 99,995 controls ridiculous?
...
written 8 weeks ago by
curious • 470
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... This seems to make no different in terms of getting this to work but thanks for taking the time ...
written 8 weeks ago by
curious • 470
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5 follow
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... `parallel bcftools stats chr{}.bcf | grep "number of records:" | cut -f 4 > chr{}.txt ::: {1..22}`
This does not seem to work for me, I have encountered similar issues with bcftools utilities and gotten around it by specifying my output with `-o` instead of `>` where possible, but obviously ...
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... Let me know if this is off topic, I considered stack exchange, but I was worried about the domain specific content.
I am performing association tests between a binary disease outcome a large set of multiallelic sites, each having *m* alleles with *Allele* representing the allelic dosage (0,1,2). I ...
written 9 weeks ago by
curious • 470
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