![]() extract-if-info/-exclude-if-info now support comparison against the empty-string value (specify ' ' as the value). psam files has been changed to male, due to having >30x fewer heterozygous calls on chrX (outside the pseudoautosomal regions) than average for females in the hg38 callset, no autosomal evidence of inbreeding, the largest fraction of non-SNPs among its chrX heterozygous calls, and the largest percentage decline in chrX heterozygous call count from build 37 to 38.Ĩ Jan: BCF import/export now permits non-Flag INFO keys to have no value, as allowed by the VCFv4.3 specification, and handles empty-String values properly. The sex of sample HG03511 in the 1000 Genomes pedigree-corrected. ![]() ![]() ![]() (Why? Because we overlooked this detail when processing the preliminary 1000 Genomes hg38 callset.) A warning, which will be upgraded to an error in the future, is now printed when nonfounders remain during these operations, and neither -nonfounders nor -ac-founders is specified. ac-founders flag added to confirm intentional exclusion of nonfounders from -mac/-max-mac/"-freq counts". pca now prints a more informative error message when there is a nan in the GRM.ĩ Jan: -sample-counts multiallelic-variant heterozygous-haploid bugfix. Linux builds now avoid requesting more memory than reported by /proc/meminfo's 'MemAvailable' entry (when it exists). glm 'omitted' optional column set added, listing only the omitted allele this (and 'a1freq') will be included in the default column set in the future. : Fixed -hardy/-hwe bug that could cause a segfault when chrX and multiallelic variants are present, and sex information is absent. ![]() 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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