Comments (1)
PLINK normally ignores all female Ychr genotypes. One workaround, if your .bim file uses "24" or "chr24" to represent the Y chromosome, is to temporarily increase the number of autosomes with e.g. "--chr-set 24".
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Related Issues (20)
- 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
- PLINK v1.9 `sprintf()` compilation warnings: Does a way to silence/fix them exist? HOT 3
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