chrchang / plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

https://www.cog-genomics.org/plink/2.0/

chrchang/plink-ng Issues

`--keep` does not handle IID-only files properly when the main dataset contains FIDs
Closed 4 months ago3
Error: Duplicate phenotype/covariate ID
Closed 4 months ago1
PLINK 1.9: Issues with --make-bed and empty .fam file
Closed 4 months ago1
clumping
Closed 5 months ago
--homozyg-group question
Closed 5 months ago1
pgenlibr: ReadList question
Closed 5 months ago7
Request for pgen files to include a version number in the header
Updated 5 months ago8
Problem with combining different samples into a single plink 1 file for later input
Closed 5 months ago1
PLINK v1.9 `sprintf()` compilation warnings: Does a way to silence/fix them exist?
Updated 5 months ago3
Persistent download URLs for built binaries?
Closed 6 months ago2
how to install in arm64 ? thks
Updated 6 months ago4
Obtaining different results from the same data in different formats
Closed 6 months ago2
plink2 --update-name issue
Closed 8 months ago1
Logistic regression returns NAs output---FIRTH_CONVERGE_FAIL
Closed 8 months ago1
Compilation failure
Closed 8 months ago1
Pgenlib 0.90.1 is not installable from PyPI with Python 3.12.2 on Mac aarch64
Closed 8 months ago1
can plink handle vcf files with * notation?
Closed 9 months ago1
File read error when converting .vcf to PLINK .ped and .map file
Closed 9 months ago1
Can't run anny PLINK command on Ubuntu 22.04
Closed 9 months ago1
Request: plink2 --extract/exclude-if-info [key(s)...]
Updated 10 months ago1
plink2 --sample-count running out of memory
Closed a year ago5
CentOs7.9 install plink1.9 error
Updated 10 months ago3
Feature Request: Upstream Dockerfile
Updated a year ago
Multithread-only --glm floating point exception
Updated a year ago2
pgenlibr: multi-threading?
Updated a year ago1
`Error: Non-concatenating --pmerge[-list] is under development.`
Updated a year ago7
--score precision error
Closed a year ago3
0 phenotype values present after --pheno.
Closed a year ago1
Overly general "--bcf file could not be scanned twice"
Updated a year ago
plans to get pgenlib on bioconda?
Closed a year ago2
CNV-SNP LD
Closed a year ago2
Python API import errors with latest version
Closed a year ago5
ERROR: compilation failed for package 'pgenlibr'
Closed a year ago8
Error: No entries in phenotype.txt correspond to loaded sample IDs.
Closed a year ago1
A question about --a1-allele
Closed a year ago1
Document mapping of chromosomes to numeric codes with --output-chr 26
Closed a year ago1
--score with mean imputation calculates allele frequency for unneeded alleles
Closed a year ago3
[pgenlib] support for `int8_t` in `read_alleles` and `read_alleles_and_phasepresent`
Closed a year ago8
Correctness in Ref/Alt when converting to VCF
Closed a year ago4
Adding columns from VCF into plink result files
Closed 2 years ago1
Specifying pairs for IBD estimation
Closed 2 years ago2
Plink2 round-tripping vcf->pgen->vcf does not preserve contig names
Updated 2 years ago3
read haploid dosages with pgenlib
Updated 2 years ago5
Error: REF allele on line 1071 of --pgen-diff .pvar file conflicts with loaded REF allele
Closed 2 years ago1
sysconf(_SC_NPROCESSORS_ONLN) should not be used
Closed 2 years ago6
problem about plink2
Closed 2 years ago1
Clarification in `pgen_spec`: what bytes goes into "variant record length" in PGEN header?
Closed 2 years ago2
How to get 0x55 in pgen_spec?
Closed 2 years ago2
Feature request: check for presence of e.g. --keep-fam file before converting to temporary psam/pvar/pgen
Closed 2 years ago1
Error: .pgen file read failure: File appears to be corrupted.
Closed 2 years ago22