Moderator: chrchang523

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chrchang5237.6k
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Posts by chrchang523

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Comment: C: Comparison of allele frequencies between population
... Oh, that's because you downloaded the sites VCF instead of the full genotypes VCF. Download a .genotypes.vcf.gz file from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ instead, or the plink2-formatted version from https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 . ...
written 16 days ago by chrchang5237.6k
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Comment: C: bcf convert 23andme to vcf
... Note that ALL of the solutions here have the same limitation as plink. It’s impossible to report an ALT allele if it simply isn’t in the data; you need an additional SNP database file. It’s only REF alleles that can be reliably filled in without that (with plink, you’d use plink2’s —ref-from-fa fl ...
written 17 days ago by chrchang5237.6k
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Comment: C: Filtering multi-allelic sites in VCF files
... Ok, sorry, I should have looked more carefully at the rest of the post. If these thrown-out ALT alleles really are just sequencing errors, this approach is ok. My comments were directed at the case where the ALT alleles were rare but not errors. ...
written 19 days ago by chrchang5237.6k
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Comment: C: Filtering multi-allelic sites in VCF files
... You almost certainly should be excluding the affected samples from your allele frequency denominators. Your approach does not do that. ...
written 20 days ago by chrchang5237.6k
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Comment: C: Filtering multi-allelic sites in VCF files
... Note that this effectively replaces all observations of rare alleles with observations of reference alleles, when it's usually more appropriate to replace the affected genotypes with "./.". ...
written 21 days ago by chrchang5237.6k
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Comment: C: Comparison of allele frequencies between population
... The pedigree file contains some samples that were excluded from the phase 3 VCF, but that's okay, the extra sample IDs will just be ignored by --keep. ...
written 21 days ago by chrchang5237.6k
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Answer: A: Comparison of allele frequencies between population
... 1. Download the pedigree file from https://www.internationalgenome.org/faq/can-i-get-phenotype-gender-and-family-relationship-information-samples/ . 2. Define your European subpopulation, and create a file with just the sample IDs within that subpopulation with e.g. a short shell script. 3. Compute ...
written 22 days ago by chrchang5237.6k
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Comment: C: how to merge two vcf files and calculate allele frequencies
... "Not exactly .vcf format" completely changes the question. I am deleting it. ...
written 4 weeks ago by chrchang5237.6k
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Answer: A: Does anyone know what test or model is being used to calculate the regression co
... --gxe performs a simple linear regression for each group, and then uses the Z-statistic in equation (4) of [Using the Correct Statistical Test for the Equality of Regression Coefficients][1] to test for equality of coefficients. [1]: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.458.9 ...
written 5 weeks ago by chrchang5237.6k
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Comment: C: Correct command line syntax for plink2
... 1. No .ped file is required (and .ped files should almost always be avoided in 2020 since they're horribly inefficient; this is why `--file` has been deliberately excluded from all plink 2.0 alpha builds). Use `--bfile` instead of `--file` to load the .bed + .bim + .fam fileset. 2. With that said, ...
written 5 weeks ago by chrchang5237.6k

Latest awards to chrchang523

Scholar 9 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 9 days ago, created an answer that has been accepted. For A: Question about re-coding SNPs in PLINK
Good Answer 17 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?
Teacher 4 weeks 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 10 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 3 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 3 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 4 months ago, created an answer that has been accepted. For A: Question about re-coding SNPs in PLINK
Teacher 4 months 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: SNP-set enrichment in GWAS analysis
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Scholar 7 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Commentator 7 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 7 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 7 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 7 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Good Answer 7 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 7 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 8 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 9 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis

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