User: chrchang523

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chrchang5232.8k
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Posts by chrchang523

<prev • 261 results • page 1 of 27 • next >
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Answer: A: VCF with SNP- count number of 100% missing genotypes
... You can dump the list of SNPs which are less than 100% missing, and then --exclude that list. ...
written 4 hours ago by chrchang5232.8k
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Comment: C: How do I remove duplicated by position SNPs using PLink?
... `--list-duplicate-vars`'s `ids-only` modifier bridges the gap with `--exclude`. The `--merge-equal-pos` flag causes variants with identical positions to be merged, keeping the IDs in the first file. However, this is conservative: if there's a single pair of same-position variants which have more t ...
written 18 days ago by chrchang5232.8k • updated 18 days ago by Ram12k
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Comment: C: How do I remove duplicated by position SNPs using PLink?
... Oh, sorry, "suppress-first" is a --list-duplicate-vars modifier, not an --exclude modifier. You also want to include "ids-only" in your --list-duplicate-vars step when your goal is just to generate a file for --exclude's use. So, the following should work: plink --bfile HighDensity --list-dup ...
written 19 days ago by chrchang5232.8k
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Comment: C: How do I remove duplicated by position SNPs using PLink?
... "suppress-first" is misspelled in your command line. ...
written 19 days ago by chrchang5232.8k
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Answer: A: Plink filtering with physical position using a text file
... plink "--extract range [filename]" can do this. The input file is expected to have chromosome IDs in the first column, [first bp, last bp] (ok for these values to be identical) in the second and third columns, and arbitrary range IDs in the fourth column. ...
written 19 days ago by chrchang5232.8k
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Answer: A: Non parametric quantitative genome wide association tests
... One possible workaround is quantile-normalizing your phenotype (forcing it to a normal distribution, keeping its rank-order). PLINK 2.0 has the --quantile-normalize flag for this, and this should be straightforward to do in R/Python/etc. as well. ...
written 23 days ago by chrchang5232.8k
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Answer: A: PLINK 1.9 mendel errors trios
... Try setting all your family IDs to "0". The paternal/maternal ID columns can only be used to identify duos/trios when family IDs match. ...
written 5 weeks ago by chrchang5232.8k
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Comment: C: Recode to VCF with -a2-allele flag in PLINK
... Hmm, the only way you should get "0 assignments made" is if the variant IDs in reference_alleles.txt don't match those in test.map. What do the first lines of test.map look like? Can you post the full .log file from a failing --a2-allele run? ...
written 5 weeks ago by chrchang5232.8k
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Answer: A: logistic regression with PLINK
... With plink 1.9, "--freq case-control" stratifies the allele frequency report by disease status. With plink 2.0, you can embed case/control allele counts directly in the logistic regression report by adding "cols=+totallelecc" after --logistic/--glm. (Note that since these are allele counts, not sa ...
written 6 weeks ago by chrchang5232.8k
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Answer: A: How to convert vcf to 23andme format
... There are two problems here. 1. The 23andMe format does not support multi-character alleles; you must reorganize your data so that none of these remain. Split length-preserving multi-nucleotide variants into a bunch of single-nucleotide variants. (As for length-changing variants, 23andMe has hist ...
written 7 weeks ago by chrchang5232.8k

Latest awards to chrchang523

Good Answer 19 days 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 weeks 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: Alternetive to GoldenHelix GWAS
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 6 weeks ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 10 weeks ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 12 weeks ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: PLINK 1.90 alpha
Scholar 3 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Teacher 3 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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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Appreciated 5 months ago, created a post with more than 5 votes. For A: Alternetive to GoldenHelix GWAS
Scholar 5 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 6 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Scholar 6 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
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Scholar 8 months ago, created an answer that has been accepted. For A: Plotting file eigenvec

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