Comments (3)
chrchang
commented on August 17, 2024
1
https://www.cog-genomics.org/plink2 has always pointed to the v1.9 documentation. I realize this is confusing since only v2.0 has a binary named "plink2"--should have planned ahead more--but note that the URL displayed on the first line ends in plink/2.0/ instead, and if you download a new v1.9 build the displayed URL ends in plink/1.9/.
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dwuab
commented on August 17, 2024
1
@chrchang Thanks for the clarifications. I will use PLINK v1.9 for the time being.
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chrchang
commented on August 17, 2024
plink2 alpha builds are intended to be a companion to, rather than a replacement for, the v1.9 binary. In particular, plink2's --make-king-table command is not a full substitute for --genome (no Z0/Z1/Z2 estimates), but if you're just interested in PI_HAT it's usually a significant improvement.
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Related Issues (20)
- 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
- plink2 --sample-count running out of memory HOT 5
- Feature Request: Upstream Dockerfile
- CentOs7.9 install plink1.9 error HOT 3
- how to install in arm64 ? thks HOT 4
- Request: plink2 --extract/exclude-if-info [key(s)...] HOT 1
- Compilation failure HOT 1
- Can't run anny PLINK command on Ubuntu 22.04 HOT 1
- File read error when converting .vcf to PLINK .ped and .map file HOT 1
- Request for pgen files to include a version number in the header HOT 8
- can plink handle vcf files with * notation? HOT 1
- Pgenlib 0.90.1 is not installable from PyPI with Python 3.12.2 on Mac aarch64 HOT 1
- Logistic regression returns NAs output---FIRTH_CONVERGE_FAIL HOT 1
- plink2 --update-name issue HOT 1
- Obtaining different results from the same data in different formats HOT 2
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