Moderator: chrchang523

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chrchang5237.3k
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Posts by chrchang523

<prev • 616 results • page 1 of 62 • next >
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Answer: A: Unrecognized flag in Plink2
... plink 2.0 is still under development. Features which enable workflows that were previously impossible with plink have been prioritized over things that already work perfectly well in plink 1.9. You should use plink 1.9 for now. ...
written 2 days ago by chrchang5237.3k
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Comment: C: Operation timed out
... (This error doesn’t involve plink, so you should keep this post and delete the plink2-users post.) ...
written 8 days ago by chrchang5237.3k
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Comment: C: How to extract a subset of samples from plink .bed files
... The number of digits is different. From what you have posted, there is every reason to believe you made a mistake creating this --keep-fam file, and your problem will go away when you fix that mistake. ...
written 11 days ago by chrchang5237.3k
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Comment: C: How to extract a subset of samples from plink .bed files
... Look closely at your --keep-fam file. The IDs are slightly off: "204117..." instead of "20417...". ...
written 11 days ago by chrchang5237.3k
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Comment: C: How to extract a subset of samples from plink .bed files
... Order does not matter. If you need help figuring out what happened, please post the .log file from the problematic run, along with the top lines from your .fam file and the —keep-fam file you used. ...
written 11 days ago by chrchang5237.3k
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Comment: C: Plink2 Linear Regression for Binary phenotypes
... If you don't have missing genotypes, the 'cc-residualize' modifier implemented in July 2020 is a better way to trade off a little accuracy for speed. ...
written 12 days ago by chrchang5237.3k
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Answer: A: Plink2 Linear Regression for Binary phenotypes
... This is by design, since logistic/Firth regression is almost always more appropriate for binary phenotypes. See https://en.wikipedia.org/wiki/Statistical_model_specification for some context. You can override this by recoding the phenotype from {1, 2} to e.g. {2, 3}, but this is very strongly disc ...
written 13 days ago by chrchang5237.3k
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Answer: A: Plink altering VCF IDs
... plink 1.x requires two-part sample IDs, so there are some rough edges re: import/export of single-part sample IDs. See https://www.cog-genomics.org/plink/1.9/input#double_id and https://www.cog-genomics.org/plink/1.9/data#recode for details. Two workarounds: - Add "--const-fid 0 [--keep-allele-o ...
written 27 days ago by chrchang5237.3k
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Comment: C: Correct way to convert plink files to vcf assigning the correct reference allele
... Possible causes of the 36 variants: - Contigs not present in or named differently in the .fasta file (how is the pseudoautosomal region encoded?) - Indels - Strand-flips (arguably the most annoying) As for the warning, it should go away if you tweak the --ref-from-fa part of the command to "--fa h ...
written 4 weeks ago by chrchang5237.3k
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Answer: A: How to check if a word is present in a column of a .ped file
... cat my.ped | cut -f 2 | grep -q "MAL-007" if [ $? -eq 0 ] then echo "yes" fi ...
written 5 weeks ago by chrchang5237.3k

Latest awards to chrchang523

Scholar 3 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 24 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 24 days ago, created an answer that has been accepted. For A: Question about re-coding SNPs in PLINK
Scholar 27 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 3 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 3 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 3 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 3 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Good Answer 3 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 4 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 4 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 5 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
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?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 5 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 5 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 5 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 5 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
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?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files

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