User: chrchang523

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chrchang5232.6k
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Posts by chrchang523

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Comment: C: lgen to ped using plink
... Wrote a response earlier, but it seems to have disappeared. The main issue is that your .map file is unsorted; plink will sort it by position before generating the new .ped + .map fileset, and I'm guessing that's why there appears to be a discrepancy. Also, it doesn't look like you posted the enti ...
written 9 days ago by chrchang5232.6k
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Comment: C: illumina genotype reports _lgen to ped using plink
... Well, it doesn't look like you posted the entire .lgen or .map files (only 4 variants, when the .log clearly indicates there were 10), so there's no way to tell if they match. Note that the .map file you did post has out-of-order variants, and plink automatically sorts them by position before gener ...
written 9 days ago by chrchang5232.6k
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... Yes, that should work. ...
written 11 days ago by chrchang5232.6k
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... refcol is the column number of the alleles you want to treat as reference; in this case, 1. IDcol is the variant ID column number; in this case, 2. ...
written 12 days ago by chrchang5232.6k
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Answer: A: Forcing A1/A2 alleles in PLINK in a VCF phased file
... - If you want to preserve phase information, you'll need plink 2.0; this is impossible in 1.9 due to the limitations of the core file format. - "--ref-allele force ancestral_snps.txt" should work. Depending on the layout of the ancestral_snps file, you might need to specify some column numbers too ...
written 12 days ago by chrchang5232.6k
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Comment: C: illumina genotype reports _lgen to ped using plink
... This is downloadable from https://www.cog-genomics.org/plink/1.9/ . (As for why plink 2.0 doesn't have the --file flag yet, that's lower priority because plink 1.9 already has a good implementation. The first development priority is enabling important things that can't be done at all with plink 1. ...
written 14 days ago by chrchang5232.6k
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Answer: A: illumina genotype reports _lgen to ped using plink
... That build had a .lgen loading bug which was fixed the following month; retry with a newer plink 1.9 build. ...
written 14 days ago by chrchang5232.6k
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Comment: C: what is 0 in the plink .bim file under allele1/2 column?
... Consider the simplest case, where you have just one sample. Whenever the sample has a homozygous call, you'll only see one allele code. Whenever it has a missing call, you won't see any allele codes. ...
written 28 days ago by chrchang5232.6k
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Answer: A: what is 0 in the plink .bim file under allele1/2 column?
... In a .ped + .map fileset, it's possible for a variant to have only one distinct allele (everyone's A A or 0 0), or even zero (everyone's 0 0). If a .bim file is generated from this type of data, it'll have 0 in place of each unknown allele code. ...
written 29 days ago by chrchang5232.6k
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Comment: C: ld matrix in plink
... If you want the matrix to just contain the SNPs in samplesnp.txt, use --extract instead of --ld-snp-list. ...
written 4 weeks ago by chrchang5232.6k

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