Moderator: chrchang523

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chrchang5235.5k
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Posts by chrchang523

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Comment: C: GWAS on dosage data - interaction
... plink 2.0 —glm handles dosage data and interactions. ...
written 9 days ago by chrchang5235.5k
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1
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Answer: A: PLINK : Error: --tdt requires a case/control phenotype.
... The first six lines are okay, but plink has told you that at least one of the other 310 lines is not okay. Find and fix the problem. ...
written 10 days ago by chrchang5235.5k
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Comment: C: Duplicate Variant IDs Issue
... plink 1.9 --bmerge, used to merge a dataset with *itself*, might do what you want here. ...
written 10 days ago by chrchang5235.5k
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Comment: C: Duplicate Variant IDs Issue
... 1. If you're fine with super-long variant IDs, you could instead add e.g. "`--new-id-max-allele-len 1000`" to your --set-all-var-ids command line. 2. "`--rm-dup retain-mismatch`" can be used to keep all instances of the duplicated SNP when the genomic data isn't identical, while writing those IDs to ...
written 16 days ago by chrchang5235.5k
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Answer: A: Duplicate Variant IDs Issue
... PLINK2's [--rm-dup flag][1] addresses actual duplicate SNPs, and the --set-all-var-ids flag you mention should assign unique IDs to same-rs# records which are actually different in your dataset. [1]: https://www.cog-genomics.org/plink/2.0/filter#rm_dup ...
written 21 days ago by chrchang5235.5k
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Answer: A: How does plink compute n_geno ("number of potentially valid call(s)")?
... This should just be the total number of variants, minus chrY for females. ...
written 5 weeks ago by chrchang5235.5k
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Comment: C: fcGENE error during conversion from .ped to .gen
... You can just use plink "--recode oxford" for this. With plink 2.0, this also works with dosage data. ...
written 6 weeks ago by chrchang5235.5k
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... No, because it's irrelevant. You noted in your plink2-users post that this only affected homozygous genotypes, which don't have a phasing state at all. plink2 renders homozygous genotypes in VCFs with '|' iff the previous heterozygous genotype was phased. (There are plans to add support for VCF " ...
written 6 weeks ago by chrchang5235.5k
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Answer: A: PLINK - error in --make-bed
... ‘0’ is normally the missing-genotype code. The body of a .ped line is supposed to look like “A C A A T G ...”. ...
written 8 weeks ago by chrchang5235.5k
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Comment: C: is fortran still used in bioinformatics?
... Among other things, I write high-performance linear algebra code. I frequently read the LAPACK documentation, and am not hopeless at reading Fortran. I stand by what I wrote. This guy has not decided on a research problem yet; they are still making a higher level choice. A large time investment ...
written 9 weeks ago by chrchang5235.5k

Latest awards to chrchang523

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 9 days ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Good Answer 15 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?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: PLINK 1.90 alpha
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
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 10 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Appreciated 10 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 10 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?
Scholar 10 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 12 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Appreciated 3 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 3 months ago, created an answer that has been accepted. 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'
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
Teacher 4 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'
Scholar 4 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'

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