Moderator: chrchang523

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chrchang5233.1k
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Posts by chrchang523

<prev • 286 results • page 1 of 29 • next >
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Answer: A: Convert VCF to BGEN 1.3
... plink2 supports allelic dosages, not genotype probabilities. So if your VCF GP field says P(0/0)=0.2, P(0/1)=0.52, P(1/1)=0.28, plink2 will just save "dosage(1)=1.08", and then when it's asked to export to BGEN it'll encode the dosage as P(0/0)=0, P(0/1)=0.92, P(1/1)=0.08. When this is fine, plink ...
written 2 days ago by chrchang5233.1k
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60
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Answer: A: getting unlinked variants and PCA analysis
... PLINK's --indep-pairwise command for selecting approximately-unlinked variants should have no problem with haploid data. However, you'll want to perform the actual PCA with another script/tool, since the variance-normalized similarity formula used by PLINK --pca only works properly for diploid data ...
written 3 days ago by chrchang5233.1k
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Answer: A: plink: vcf to ped
... The plink 1.9 command should work. If it didn’t, can you post the .log file from that run? The plink2 —recode command doesn’t work yet, because it’s an incomplete program in alpha testing, and .ped + .map support is a lower development priority since you can always use —make-bed followed by plink ...
written 4 days ago by chrchang5233.1k
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Comment: C: Merlin format, Mach, Plink, Plink2, and best practices of snp imputation
... In your position, I'd use plink 1.x except when you run into something that's impossible to do with v1.x, but possible with v2. Unfortunately, direct conversion to or from Merlin format is not supported by any version, due to a timing quirk (Merlin format was kind of obsolete when plink 1.07 was re ...
written 4 days ago by chrchang5233.1k
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Comment: C: Merlin format, Mach, Plink, Plink2, and best practices of snp imputation
... Is it really necessary to use mach1? Imputation software has advanced considerably since 2010, and newer packages support more commonly-used formats than Merlin. As for plink2 and --file, that doesn't work yet because plink2 is an incomplete program currently undergoing alpha testing. The main pr ...
written 4 days ago by chrchang5233.1k
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Comment: C: Genetic variation data analysis frequently tricky problems and troubleshot
... For #2, what version of plink are you running? All builds in the last ~3 years support ./. and (with the appropriate —vcf-half-call setting) ./0 . ...
written 21 days ago by chrchang5233.1k
1
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Answer: A: 1000 Genome Project VCF file and Plink file
... While the project continued for a few years past May 2013, they froze their official variant calls at that point. If you're performing an analysis that just requires subpopulation minor allele frequencies and/or similar summary statistics, gnomAD is probably more useful now. But yes, if you're loo ...
written 23 days ago by chrchang5233.1k
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Comment: C: gender assignment sex-check in Plink
... This depends on the set of variants in your dataset. E.g. if you have lots of rare MAF < 5% variants, the average female het rate will be far less than 20%. The F-statistic helps correct for this, but its distribution will still depend on dataset-specific details. However, you can count on mal ...
written 23 days ago by chrchang5233.1k
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Comment: C: gender assignment sex-check in Plink
... It's based on the same heterozygosity/inbreeding coefficient as --het. ...
written 23 days ago by chrchang5233.1k
1
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784
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Answer: A: Dosage data single probability to PLINK format
... 1. Use plink 2.0’s —import-dosage and —make-bed flags to generate plink bed/bim/fam files. —hard-call-threshold can be used to control which dosage values get rounded to the nearest integer vs. converted to a missing call. 2. plink 1.x’s —recode command converts bed/bim/fam to ped/map. ...
written 6 weeks ago by chrchang5233.1k

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Scholar 2 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
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Scholar 6 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
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