Moderator: chrchang523

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chrchang5234.6k
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Posts by chrchang523

<prev • 389 results • page 1 of 39 • next >
4
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185
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Answer: A: Fast way to return genomic regions for 10,000 SNPs in rsID
... It's a hack, but if you use e.g. awk to add a fake sample + genotype column (could be all "./.") to your rsID VCF file, you can then use plink2 --vcf All_20180423.vcf --extract my_rsids.txt --export vcf to generate a VCF with only the rsIDs you care about, and it's straightforward to finish th ...
written 3 days ago by chrchang5234.6k
1
vote
1
answer
63
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1
answers
Answer: A: How to process Plink2 --score across chromosomes
... You can use —out to make your per-chromosome runs write to different output files. ...
written 4 days ago by chrchang5234.6k
1
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1
answer
91
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1
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Answer: A: PLINK --r2 square: snp ids are not written
... You can use e.g. --write-snplist for that. ...
written 6 days ago by chrchang5234.6k
1
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2
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103
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2
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Answer: A: Error: --score takes at most three numeric parameters.
... Sorry about the inappropriate error message; I'll fix that in the next build. The actual issue is that plink2 --score replaces the 'sum' modifier with direct control over the output columns. "plink2 --help score" has the following text toward the end: The main report supports the following ...
written 6 days ago by chrchang5234.6k
2
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1
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96
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1
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Answer: A: PLINK dosage data - convert and/or read in R
... Convert to hard-calls: "plink2 --pfile ... --make-bed --out ..." Convert to an R-readable form: "plink2 --pfile ... --export A-transpose --out ..." ...
written 7 days ago by chrchang5234.6k
2
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1
answer
83
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1
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Answer: A: Plink2. psam file missing in 1000G Phase3
... "(Quick start: just download the three boldfaced links, and then decompress the .pgen.zst.)" Look for the third boldfaced link on the top of the page. ...
written 7 days ago by chrchang5234.6k
2
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0
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84
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0
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Comment: C: Plink Error: Duplicate ID 'chr:pos:A1:A2' generated by --set-missing-var-ids
... You're much better off using plink 2.0 for this operation, since (i) it lets you specify REF/ALT alleles when constructing the IDs, avoiding the duplicate indel problem, and (ii) it forces you to specify how very long allele codes should be handled instead of silently truncating them, preventing som ...
written 18 days ago by chrchang5234.6k
1
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1
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151
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1
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Comment: C: Plink2 error: Skipping --glm regression on phenotype 'PHENO1' since variance inf
... Oh, I should have also noted that year-of-birth and age are almost totally redundant; you need to remove one of those covariates. ...
written 19 days ago by chrchang5234.6k
0
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1
answer
829
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1
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Comment: C: "Error: --recode 23 cannot be used with multi-character allele names." when conv
... Actually, plink can handle indels, it's the 23andMe format which can't really represent them. ...
written 21 days ago by chrchang5234.6k
0
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1
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138
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1
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Answer: A: Plink unable to read plink.dosage.gz file
... The problem is that you are still using plink 1.07 for dosage analysis. plink 2.0 can read VCF dosages directly, and supports the full range of linear/logistic regression options on dosage data rather than the limited set offered by plink 1.x --dosage. ...
written 21 days ago by chrchang5234.6k

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