Moderator: chrchang523

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chrchang5233.7k
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Posts by chrchang523

<prev • 328 results • page 1 of 33 • next >
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Answer: A: VCF to Bed file format using GATK
... Is there any reason you need to use GATK for this? Just use "plink --vcf [filename] --make-bed". ...
written 3 days ago by chrchang5233.7k
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Answer: A: Keeping both A1/A2 in PLINK for assoc/logistic output
... Use plink 2.0 --glm for this; it gives you a lot more flexibility re: what columns are included in the output, and by default both alleles are shown (and there's a third column indicating which allele is currently being regressed on). ...
written 6 days ago by chrchang5233.7k
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Comment: C: Why my pvalue histogram doesn't have uniform distribution
... This is expected if your sample sizes are such that p-value 1 usually corresponds to mid-p value in the 0.95 bin. ...
written 12 days ago by chrchang5233.7k
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Answer: A: Why my pvalue histogram doesn't have uniform distribution
... The large number of p=1 observations is due to p-values being "rounded up". For example, if count=200 and each row/column sums to 100, the central {50, 50} {50, 50} table has a ~11.2% chance of being observed under the null hypothesis. This table corresponds to p-value=1; the adjacent {49, 51} {51 ...
written 13 days ago by chrchang5233.7k
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Answer: A: Estimate relatedness in large dataset
... With plink 2.0, "plink2 --vcf [VCF filename] --make-king-table --king-table-filter 0.177" is very good at detecting first-degree relationships (use a lower --king-table-filter cutoff if you also want to estimate more distant relationships). If you want to follow that up with more sophisticated rela ...
written 13 days ago by chrchang5233.7k
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Answer: A: Genotype frequency per sample
... "plink --file ... --het" will give you the number of Aa calls for each sample. If you also need AA/aa, you'd need to define which alleles are A and which ones are a. Once you have, you can merge in a synthetic sample with all aa calls, use --merge to merge that sample with your real dataset, and t ...
written 13 days ago by chrchang5233.7k
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Answer: A: PCA implementation in plink
... plink constructs the variance-standardized genetic relationship matrix ("GRM"; see Yang J, et al. "GCTA: A Tool for Genome-wide Complex Trait Analysis" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014363/ for some discussion), and extracts the top principal components from that matrix. ...
written 13 days ago by chrchang5233.7k
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Answer: A: What are the major differences between plink and plink2?
... Sorry about not noticing this earlier. The main difference is that plink 1.9 is essentially finished, while plink 2.0 is an alpha-stage program which will have significant unfinished components for a while to come. As a consequence, current development priorities for plink 2.0 are centered around ...
written 13 days ago by chrchang5233.7k
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Answer: A: Info Score > 1 Plink?
... The INFO field in an .assoc.dosage file contains the MaCH r-squared imputation quality metric, which is [observed dosage variance] / [expected variance, given observed allele frequencies and Hardy-Weinberg equilibrium]. Despite the r-squared name, this is not guaranteed to be less than or equal to ...
written 19 days ago by chrchang5233.7k
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Comment: C: Info Score > 1 Plink?
... INFO has the same meaning in both files, but that documentation snippet is actually for a slightly different (and defunct) command, --proxy-assoc instead of --dosage. ...
written 19 days ago by chrchang5233.7k

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Teacher 14 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
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