![]() ![]() -set-all-var-ids and related flags are now applied to all -pmerge inputs.-allow-extra-chr is never necessary anymore unless -strict-extra-chr is specified.(alpha 6): This makes the following potentially compatibility-breaking changes: These bugfixes has been backported to alpha 5. Fixed a -glm chrX/chrY -parameters + -tests bug. sort-vars can handle larger INFO columns than it could yesterday.Ģ Oct: Fixed -sort-vars bug that could occur when INFO column didn't fit in memory, and improved performance in that case (though a bit of extra disk space is now required). Affected code paths are now disabled in alpha 5.ģ Oct: -sort-vars + -make-just-pvar now works properly instead of segfaulting. 1000 Genomes hg38 callset on the Resources page now has dbSNP 156 rsIDs if you want them.ġ1 Oct: Fixed a -clump/-ld phased-dosage bug. (The old flag name will still work in all PLINK 2.0 builds.) The -set-hh-missing flag has been renamed to -set-invalid-haploid-missing, to make the name more accurate. These bugfixes have been backported to alpha 5. A related exception is -score and -variant-score when they perform mean-imputation these now block you from processing chrY variants when unknown-sex samples are present.įixed a -variant-score chrY bug, and a -ld chrX unknown-sex handling bug. (Yes, this is a potentially compatibility-breaking change.) The main exception is missingness-rate in that case, use the new -y-nosex-missing-stats flag to include them. These bugfixes have been backported to alpha 5.ġ8 Oct: Most computations now consider unknown-sex samples on chrY, unless they explicitly stated otherwise. Alpha 5 has been updated with the -clump-unphased bugfix dosages + -clump phased-r 2 was already disabled.Ģ4 Oct: Fixed -clump no-males chrX segfault, and -clump-unphased bug that could occur when dosages and fully-missing values were simultaneously present. (Results are unchanged when dosages are not present.) Fixed -clump-unphased chrX bug. Fixed -clump chrX missing-data bug.Ģ7 Oct: Phased-r 2 (computed by -clump when -clump-unphased is absent, as well as the upcoming -r-phased command) formula has been changed to remove an inappropriate independence assumption that caused the r 2 of a variant with itself to be less than 1 when dosages were present. This bugfix has been backported to alpha 5.Ģ9 Oct: Fixed -clump crash that could occur if the total number of alleles in the dataset was a multiple of 64 (or 32 for 32-bit builds) this bugfix has been backported to alpha 5. These bugfixes have been backported to alpha 5.Īffected builds and GitHub releases will be deleted in 2024.Ģ1 Oct: Fixed segmentation fault that could occur when processing multiallelic variants with 4+ alleles. vcf-require-gt should work properly with VCF files again. normalize + variant-split in the same command now causes a warning (which will be upgraded to an error in a future build) to be printed, since those operations should almost always be split across two PLINK 2 runs.Ģ1 Nov: Fixed serious -glm double-precision logistic regression bug if you performed double-precision logistic regression on a binary phenotype with a Jan-Oct 2023 plink2 build, we recommend rerunning the regression with this fix. Fixed error in phased-r 2 log-likelihood calculation that could cause a slightly suboptimal solution to be selected (occasionally changes -clump/-ld result) this fix has been backported to alpha 5.Ģ3 Nov: Fixed categorical-covariate preprocessing bug that could occur in -glm no-firth mode. Source code, compilation instructions, and the like are on the developer page. ( More detailed credits.) (Usage questions should be sent to the plink2-users Google group, not Christopher's email.) Binary downloadsġ: Intel-labeled builds can still run on AMD processors, and vice versa, but they're statically linked to linear algebra libraries optimized for the labeled vendor. PLINK 2.0 alpha was developed by Christopher Chang, with support from GRAIL, LLC and Human Longevity, Inc., and substantial input from Stanford's Department of Biomedical Data Science.
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