Moderator: chrchang523

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chrchang5236.9k
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Posts by chrchang523

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Comment: C: Plink unable to read plink.dosage.gz file
... Yes, use --covar for that. ...
written 1 day ago by chrchang5236.9k
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Comment: C: Plink unable to read plink.dosage.gz file
... This depends on how your dosages are encoded in the VCF, but something like plink2 --vcf [VCF path] dosage=DS --pheno [phenotype file] --pheno-name [phenotype name] --glm should work. ...
written 1 day ago by chrchang5236.9k
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Answer: A: Export to PLINK file
... Yes, this is a very common scenario; you just need to fill in '0' for the Father and Mother IDs. ...
written 1 day ago by chrchang5236.9k
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Comment: C: Flipping every REF/ALT and corresponsing genotypes of every single indel in a VC
... I alluded to the fact that Oxford format does not define whether REF is first or last. It looks like Eagle and Shapeit make different assumptions from each other. ...
written 3 days ago by chrchang5236.9k
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Answer: A: Flipping every REF/ALT and corresponsing genotypes of every single indel in a VC
... You should be using plink 2.0 instead of 1.9 as much as possible whenever allele order matters. Otherwise, if you forget --keep-allele-order even once, you're in trouble; and there are some plink 1.9 commands (like --linear/--logistic with interaction terms) which need to NOT be run with --keep-all ...
written 3 days ago by chrchang5236.9k
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Comment: C: PLINK: missing covariates?
... As I noted at https://github.com/chrchang/plink-ng/issues/144 , you don't have enough samples. See e.g. https://stats.stackexchange.com/questions/26016/sample-size-for-logistic-regression . ...
written 9 days ago by chrchang5236.9k
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Answer: A: PLINK is not working (bad CPU type in executable) on Mac
... Catalina does not support 32-bit applications. You should use a newer PLINK version. ...
written 10 days ago by chrchang5236.9k
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Comment: C: PCA with split up chromosomes
... PCA should be run after you've applied a MAF filter and performed LD pruning (e.g. --indep-pairwise). If per-chromosome bed/bim/fam files are small enough to be usable at the beginning, a merged all-chromosome bed/bim/fam is almost always small enough to be usable after MAF filtering and LD pruning ...
written 15 days ago by chrchang5236.9k
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Comment: C: Plink with hwe option does not work
... Please post the full .log file (or console output) from your failing run. ...
written 17 days ago by chrchang5236.9k
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Answer: A: Plink 1.9 haplotype blocks with not phased data
... Yes, —blocks is designed for unphased data. ...
written 18 days ago by chrchang5236.9k

Latest awards to chrchang523

Scholar 2 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 18 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 5 weeks ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Good Answer 5 weeks 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 6 weeks ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 6 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 6 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 7 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 8 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
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
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: How to I convert 23andMe Raw Genome to GenBank or FASTA?
Good Answer 8 weeks 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 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 9 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 11 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Good Answer 4 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 4 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 4 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Appreciated 4 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 4 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'

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