Moderator: chrchang523

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chrchang5234.9k
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Posts by chrchang523

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Comment: C: Convert IMPUTE2 to VCF while keeping phase information
... [plink 2.0][1] supports this: plink2 --haps --export vcf --out [1]: http://www.cog-genomics.org/plink/2.0/ ...
written 20 hours ago by chrchang5234.9k
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Answer: A: PLINK vcf to binary files error: Unused command line option: --vcf
... --vcf requires plink 1.9; you appear to be using plink 1.07. ...
written 5 days ago by chrchang5234.9k
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Answer: A: merging multiple chromosomes in a single file
... This isn't built into plink2 yet (which is why it is still in alpha testing; --pmerge is the last major function that needs to be completed before beta testing can begin). A reasonable workaround for now is to export to VCF, use "bcftools concat", and then re-import. ...
written 10 days ago by chrchang5234.9k
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Comment: C: Interpreting plink snp tagging output
... "plink2 --bfile ... --rm-dup --make-bed --out ..." This also verifies that genotypes are identical between the duplicate-ID variants (and errors out when this isn't true). "plink2 --help rm-dup" lists other options for handling genotype mismatches. ...
written 20 days ago by chrchang5234.9k
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Comment: C: Interpreting plink snp tagging output
... With plink 2.0, "plink2 --bfile ... --freq cols=+pos" will do the trick. (plink 1.9 --freq does not provide a way to add the POS column.) ...
written 21 days ago by chrchang5234.9k
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Comment: C: Interpreting plink snp tagging output
... There should be no difference, other than very rare instances of MAFs being considered to be "tied" by one version and microscopically different by the other. ...
written 21 days ago by chrchang5234.9k
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Comment: C: Interpreting plink snp tagging output
... 1. --indep and --indep-pairwise preferentially keep higher-MAF SNPs. (You can change this to an arbitrary priority order by using --read-freq to feed plink fake MAFs.) 2. Can you post your failing "--recode vcf" command line, and the full .log file? ...
written 22 days ago by chrchang5234.9k
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Answer: A: Interpreting plink snp tagging output
... It's the .prune.out SNPs which are guaranteed to have r^2 > .7 with another SNP here. A .prune.in SNPs might tag other SNPs, or it might just tag itself. ...
written 22 days ago by chrchang5234.9k
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Comment: C: Chromosome X GWAS in related individuals
... PLINK's X-inactivation model is controlled by the --xchr-model flag. "--xchr-model 2" treats male genotypes as homozygous females, and is the default in PLINK 2.0. With that said, PLINK doesn't currently have a LMM implementation. ...
written 25 days ago by chrchang5234.9k
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Answer: A: SNP IDs changed when making .ped files using PLINK
... If the chromosomal locations and rsIDs are in your VCF file, they'll also be in the .ped file generated by your plink command. I'd double-check how the R package works. ...
written 27 days ago by chrchang5234.9k

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Appreciated 15 days ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 21 days ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 5 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
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