User: chrchang523

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chrchang5232.2k
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Posts by chrchang523

<prev • 234 results • page 1 of 24 • next >
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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 6 days ago by chrchang5232.2k
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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 10 days ago by chrchang5232.2k
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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 27 days ago by chrchang5232.2k
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Answer: A: case control association analysis with covariates in plink?
... --logistic is the command you're looking for. ...
written 28 days ago by chrchang5232.2k
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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 5 weeks ago by chrchang5232.2k
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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 5 weeks ago by chrchang5232.2k
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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 5 weeks ago by chrchang5232.2k
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Comment: C: plink vcf recodeA error ALT allele duplicates REF allele
... This is because VCF import happens before everything else plink does: the entire file is imported, and only then are flags like --maf applied. Otherwise, it would be necessary to add --maf logic to every single import routine, etc. (The full order of operations is at https://www.cog-genomics.org/p ...
written 6 weeks ago by chrchang5232.2k
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Answer: A: plink vcf recodeA error ALT allele duplicates REF allele
... How was this VCF file generated? The REF and ALT alleles should never be identical; monomorphic variants should have either "." or some unobserved alternate allele in the ALT column. With that said, you can recover from this situation with a script that detects lines where the REF and ALT columns ...
written 6 weeks ago by chrchang5232.2k
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Answer: A: Obtain alleles A1 and A2 alleles from plink output
... With plink 1.9, assuming that the A2 alleles in chrom##.bim are always major (you can double-check by running "./plink --bfile ../cal/chrom## --make-bed" and verifying that the new .bim file is identical to the old one, since plink 1.x automatically flips minor A2 alleles), you can 1. Create an all ...
written 7 weeks ago by chrchang5232.2k

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