Comments (4)
chrchang
commented on June 17, 2024
That is correct; I decided to use alphabetic rather than A1/A2 order for now since plink 1.x normally doesn't try to preserve A1/A2 order. So yes, you should use a short bash script for now if you want REF/ALT-based names.
(plink 2.0 fixes this.)
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dwaggott
commented on June 17, 2024
Okay, looking forward to 2.0. Is there a dev repo?
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chrchang
commented on June 17, 2024
Not yet, but I'll let you know when that changes.
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chrchang
commented on June 17, 2024
Forgot to comment here that the plink 2.0 dev repo is now visible.
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Related Issues (20)
- plans to get pgenlib on bioconda? HOT 2
- Specifying pairs for IBD estimation HOT 2
- read haploid dosages with pgenlib HOT 5
- `Error: Non-concatenating --pmerge[-list] is under development.` HOT 7
- ERROR: compilation failed for package 'pgenlibr' HOT 8
- [pgenlib] support for `int8_t` in `read_alleles` and `read_alleles_and_phasepresent` HOT 8
- Plink2 round-tripping vcf->pgen->vcf does not preserve contig names HOT 3
- --score with mean imputation calculates allele frequency for unneeded alleles HOT 3
- Adding columns from VCF into plink result files HOT 1
- Correctness in Ref/Alt when converting to VCF HOT 4
- Document mapping of chromosomes to numeric codes with --output-chr 26 HOT 1
- A question about --a1-allele HOT 1
- Error: No entries in phenotype.txt correspond to loaded sample IDs. HOT 1
- Python API import errors with latest version HOT 5
- CNV-SNP LD HOT 2
- Multithread-only --glm floating point exception HOT 2
- Overly general "--bcf file could not be scanned twice"
- 0 phenotype values present after --pheno. HOT 1
- --score precision error HOT 3
- pgenlibr: multi-threading? HOT 1
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