User: Tao
Tao • 420
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... NO worries. Please upvote or accept my post if you think useful :) ...
written 5 months ago by
Tao • 420
0
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... There is incompatibility between options in PLINK.
I would suggest you to separate your process into two steps: --hwe, --maf are for quality control; and --chr --from-bp --to-bp are for extracting.
And --out should be prefix names of output plink files, not folder name. ...
written 5 months ago by
Tao • 420
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Answer:
A: color gradient for heatmap2
... I think you can try to remove col=bluered(100), because in default, they use yellow-red schema.
P.S. You can create a vector of n contiguous colors using the functions rainbow(n), heat.colors(n), terrain.colors(n), topo.colors(n), and cm.colors(n).
...
written 5 months ago by
Tao • 420
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... Hi, I think reference allele refers to the allele shown in the reference genome, isn't it? Please check the website: https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation/what-are-variants-alleles ...
written 5 months ago by
Tao • 420
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... That is definitely a possible way. Thanks Pierre. But if ref allele is small indel, that could be a problem. ...
written 5 months ago by
Tao • 420
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... Given the chromosome, position and A1 allele, A2 allele, how to easily tell which allele is the reference allele?
I know it is possible to extract the annotation from dbSNP, 1000G or other reference panels. But, that will need to download large mount of data. What I am looking are more efficient w ...
written 5 months ago by
Tao • 420
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... Thanks for your prompt and deep insights! ...
written 11 months ago by
Tao • 420
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... Thanks for your comments. But I am not quite understand that why plink doesn't directly count the real haplotypes from samples? since the 1000G genotypes are phased. ...
written 11 months ago by
Tao • 420
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... When I calculate the LD details between a pair of SNPs using following command as an example, why there might be two solutions shown as following (Q1)?
plink --bfile 1000G.genotypes --ld rs10005588 rs12505231
>
Solution #1:
R-sq = 0.000943758 D' = 1
Haplotype ...
written 11 months ago by
Tao • 420
• updated
11 months ago by
chrchang523 ♦ 7.3k
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... Hi, I got the same problem. That is because when you were converting plink to vcf, probably using plink --recode vcf, "The A2 allele is saved as the reference and normally flagged as not based on a real reference genome ('PR' INFO field value)." See plink explanation [here][1]. That's saying the --r ...
written 16 months ago by
Tao • 420
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