User: Sunshine n Rain

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Posts by Sunshine n Rain

<prev • 9 results • page 1 of 1 • next >
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Comment: C: In GWAS Studies, how to understand "97 SNPs explain 2.7% of BMI"?
... Hi Philipp, I think your explanation of variance explained is more like prediction accuracy (i.e., construct polygenic score (PGS) and calculate the squared correlation between PGS and phenotype from an independent target sample). In my understanding, variance explained is the proportion of variance ...
written 8 months ago by Sunshine n Rain20
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Comment: C: Effect size of a SNP - contribution to genetic variance
... My colleague told me that I misunderstood the meaning of the contribution of the locus to the genetic variance of the trait. It is not the same with the genetic variance explained by that SNP, it is just the variance of that SNP. ...
written 10 months ago by Sunshine n Rain20
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Comment: C: Effect size of a SNP - contribution to genetic variance
... Hi Collin, I think the BX represents for genetic value of one causal SNP here. The ES is not the same as Var(Y). ...
written 10 months ago by Sunshine n Rain20
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Comment: C: Effect size of a SNP - contribution to genetic variance
... Hi Peixe, In my opinion, "The effect size, as defined above, corresponds to the **contribution of the locus to the genetic variance** of the trait under Hardy-Weinberg equilibrium and an additive polygenic model (Park et al., 2010)" should be ES/Var(G) rather than the ES as they defined. Var(G) is ...
written 10 months ago by Sunshine n Rain20
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hi Kelvin, thank you very much for your tutorial. It helps me a lot to plot the PCA-bi plot of 1kg Phrase III samples. My question is, if I would like to plot my own sample's PCA with 1kg sample's PCA (My samples were genotyped by SNP array. There were around 700k SNPs. I want to check whether my ...
written 13 months ago by Sunshine n Rain20
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Comment: C: Filtering Imputation output: how to filter on a VCF INFO field
... Hi, thank you for your post. It helps me a lot with filtering dose.vcf.gz and converting them to plink format. However, I found the filtered files have far less number of rows than the files filtered by: bcftools view -i 'R2>.8 & MAF>.05' -Oz chrnum.dose.vcf.gz > chrnum.filtered.vc ...
written 15 months ago by Sunshine n Rain20
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Comment: C: check rsID of mismatched SNPs by bcftools fixref plugin
... Hi Kevin. Thanks for your answer. I decide to drop those ambiguous sites and proceed analysis. ...
written 16 months ago by Sunshine n Rain20
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Comment: C: check rsID of mismatched SNPs by bcftools fixref plugin
... Hi Kevin. Thanks for your comments. I used this unsafe command because when I used the # Swap the alleles bcftools +fixref broken.bcf -Ob -o fixref.bcf -- -d -f /path/to/reference.fasta -i All_20151104.vcf.gz command, the mismatch rate achieved 65%. I think this is because some SNPs in m ...
written 16 months ago by Sunshine n Rain20
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check rsID of mismatched SNPs by bcftools fixref plugin
... I used bcftools fixref plugin to match reference allele with GRCh37. As the result shown below, I have got 18901 unresolved SNPs. 1. Is there anyway to see the rsID of these unresolved SNPs? 2. Why are there unresolved SNPs? 3. What can I do to make these SNPs's reference allele match those ...
fixref plugin bcftools mismatch written 16 months ago by Sunshine n Rain20 • updated 15 months ago by EagleEye6.5k

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