User: chrchang523

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chrchang5232.4k
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Posts by chrchang523

<prev • 237 results • page 1 of 24 • next >
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Comment: C: Plink: Quick Way To Combine Two Datasets Using Only Common Markers
... Because the resulting merged dataset will have the union of the individual datasets' markers, and the original poster wanted the intersection. ...
written 24 days ago by chrchang5232.4k
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Answer: A: merge cases and controls with plink
... One possible workflow is described at http://www.cog-genomics.org/plink/1.9/data#merge3 . ...
written 7 weeks ago by chrchang5232.4k
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Answer: A: Convert and filter VCF by a pre-existing BIM
... Assuming your variants have unique IDs, you can use plink --write-snplist (or Unix "cut -d [delimiter] -f 2") on the .bim file to create a list of variant IDs to keep, and then plink --extract to keep just those variants in another dataset. ...
written 7 weeks ago by chrchang5232.4k
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Comment: C: Merging files in plink
... plink assumes all distinct variants have different IDs; it tries to merge all variants with the same ID. Do you have entire chromosomes of variants named '.'? ...
written 8 weeks ago by chrchang5232.4k
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Answer: A: PCA using plink files
... plink 2.0 (http://www.cog-genomics.org/plink/2.0 ) has efficient PCA implementations. For smaller datasets (let's say <5000 samples), plink2 --bfile myfile --pca 10 --out qcvcf works; larger datasets can be handled with plink2 --bfile myfile --pca approx 10 --out qcvcf ...
written 9 weeks ago by chrchang5232.4k
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Answer: A: Plink --het function and sample size
... --het requires fairly accurate allele frequencies. If you are not using --read-freq, results will depend on the allele frequencies in your immediate dataset, and will be wildly inaccurate if your dataset has few samples. ...
written 11 weeks ago by chrchang5232.4k
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Answer: A: case control association analysis with covariates in plink?
... --logistic is the command you're looking for. ...
written 11 weeks ago by chrchang5232.4k
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Comment: C: how to switch REF and ALT alleles in VCF files if the REF is incorrect according
... It depends on what your RefSeq file looks like. The basic structure of the command would be plink --vcf [name of plink-exported VCF with incorrect reference alleles] --a2-allele [name of RefSeq file] [1-based column index of ref alleles] [1-based column index of variant IDs] --recode vcf --rea ...
written 12 weeks ago by chrchang5232.4k
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Answer: A: how to switch REF and ALT alleles in VCF files if the REF is incorrect according
... Given a file with the correct reference alleles for each variant ID, you can use plink's --a2-allele flag to fix them in the VCF. ...
written 12 weeks ago by chrchang5232.4k
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Answer: A: Get LD data for any two SNPs
... "plink --r2 in-phase" provides both r-squared and directionality; see https://www.cog-genomics.org/plink/1.9/ld#r . ...
written 3 months ago by chrchang5232.4k

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