User: chrchang523

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chrchang5232.1k
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Posts by chrchang523

<prev • 224 results • page 1 of 23 • next >
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Comment: C: Inconsistency in VCF and Plink format after conversion
... Can you be more specific about an additional problem you're having with 1.9? I'm actively updating it to remove problems with replacing v1.07 with v1.9 (and this is now the only way in which v1.9 is updated; all new stuff is only going into the v2.0 codebase at this point). ...
written 3 days ago by chrchang5232.1k
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Comment: C: Inconsistency in VCF and Plink format after conversion
... Does this work if you use plink for the import instead (e.g. "plink --vcf myfile.vcf.gz --recode --out myfile_plink")? ...
written 4 days ago by chrchang5232.1k
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Comment: C: use of 2 covariate files for association analysis in plink
... With a bash script: A. Merge the FID and IID fields with something like cat orig_covar_1.txt | awk '{out=$1"_"$2; for(i=3;i<=NF;++i){out=out"\t"$i}; print out}' > covar_merged_ids_1.txt cat orig_covar_2.txt | awk '{out=$1"_"$2; for(i=3;i<=NF;++i){out=out"\t"$i}; print out}' > covar_me ...
written 16 days ago by chrchang5232.1k
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Answer: A: use of 2 covariate files for association analysis in plink
... No; you'll need to merge the files with a short script. ...
written 17 days ago by chrchang5232.1k
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Comment: C: computational tools for univariate and multivariate GWAS using quantitative trai
... PLINK currently only supports univariate models, and it is not optimized for a huge number of phenotypes in the way Matrix eQTL is. ...
written 19 days ago by chrchang5232.1k
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Comment: C: Genotype normalization: the PLINK --standard-beta flag
... For what it's worth, genotype normalization in this context is being removed in PLINK 2.0; standard-beta will only normalize covariates and quantitative phenotypes. ...
written 20 days ago by chrchang5232.1k
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Answer: A: Creating Binary file (*.bed, *.bim, *.fam file) from 1000GP legend file
... The .legend file is essentially PLINK's .bim, with a few extra columns. You also need .hap and .sample files to generate a full PLINK fileset (and you'll probably need to do some minor preprocessing on the 1000GP phase 3 .sample file to make it readable by existing tools). ...
written 6 weeks ago by chrchang5232.1k
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Answer: A: Cutting up plink .ped/fam files to create files for n genomic windows
... You can use a bash for loop which repeatedly makes plink calls of the form "plink --bfile ... --chr ... --from-kb ... --to-kb ... --make-bed --out ..." ...
written 8 weeks ago by chrchang5232.1k
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Answer: A: Require help in using PLINK flags and scripts
... "Invalid header bytes in .bed file" means that your --bfile parameter does not actually correspond to a PLINK 1 .bed file. In this case, it looks like you have a genotype fileset from IMPUTE2. Did you previously convert it to .bed+.bim+.fam, but accidentally type ".impute2" at the end here? ...
written 8 weeks ago by chrchang5232.1k
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Answer: A: Is there a way to tell PLINK and VCFtools to sort the samples in a particular or
... PLINK 1.9's --indiv-sort flag (https://www.cog-genomics.org/plink2/data#indiv_sort ) lets you do this. (If you want to export a VCF, though, you'll need to run PLINK twice, once with --indiv-sort + --make-bed, and then once with --recode vcf using the newly sorted fileset.) ...
written 9 weeks ago by chrchang5232.1k

Latest awards to chrchang523

Teacher 17 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 17 days ago, created an answer that has been accepted. For A: Plotting file eigenvec
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 4 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: How to I convert 23andMe Raw Genome to GenBank or FASTA?
Scholar 5 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
Scholar 6 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
Scholar 10 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
Appreciated 11 months ago, created a post with more than 5 votes. For A: Alternetive to GoldenHelix GWAS
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: How to I convert 23andMe Raw Genome to GenBank or FASTA?
Scholar 14 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
Appreciated 15 months ago, created a post with more than 5 votes. For A: Alternetive to GoldenHelix GWAS
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
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Scholar 16 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: PLINK 1.90 alpha
Scholar 20 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: PLINK 1.90 alpha
Scholar 20 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 21 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
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Appreciated 23 months ago, created a post with more than 5 votes. For A: Alternetive to GoldenHelix GWAS
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: PLINK 1.90 alpha

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