geno-counts, -hardy, and -hwe were affected if you used one of these flags in the same run as a sample filter (-keep/-remove, etc.) with an AVX2 build, we recommend that you rerun with this build.ġ4 May: -make-grm-bin bugfix (.grm.N.bin file contained too few entries when no missing genotypes were present). score parallelism improvement.ģ1 May: HGDP-CEPH whole-genome-sequencing genotype calls have been posted to the Resources page.ġ9 May: Fixed AVX2-build-only bug that could result in miscounting of the genotypes at the very end of a row when a sample filter was being applied. Fixed bug that could cause a -pmerge assertion failure when multiallelic variants are present in the input. ped files with less than ~21k variants if you used -pedmap on a small. bed-transpose bug which resulted in incorrect imports of. plink2_common.h now has a HIGH_CONTIG_BUILD #define that can be uncommented to extend the contig-count limit from ~65k to ~980k the "Too many distinct nonstandard chromosome/contig names" error message now mentions this.Ģ Jun: Fixed. HIGH_AUTOSOME_NUM_BUILD #define added to plink2_common.h.ģ Jun: Fixed -score dosage-processing bug in yesterday's build that could cause a segfault, and implemented more speed improvements. A warning is now printed when importing non-PLINK-format data containing chrX, and expected sex information and/or -split-par is missing this will also become an error in the future, which can be suppressed with -lax-chrx-import. vcf) this will become an error in the future, and the warning/error can be suppressed with -allow-misleading-out-arg. A warning is now printed when the -out argument ends with a common file extension (.bcf. : Fixed AVX2 -set-var-ids bug that caused spurious "Variant IDs are limited to 16000 characters" errors when the POS value for a variant was 0.ĩ Aug: Fixed -pmerge bug that could trigger when duplicate variants (identical ID, position, and alleles) were present in an input fileset.ġ Aug: Out-of-bounds -pheno-col-nums/-covar-col-nums arguments now produce an appropriate error message, instead of a segfault. Source code, compilation instructions, and the like are on the developer page. We will try to provide an AMD Zen-optimized build as soon as supporting libraries are available.Ģ: You need to have Rosetta 2 installed to run this on M1 Macs.
( More detailed credits.) (Usage questions should be sent to the plink2-users Google group, not Christopher's email.) Binary downloadsġ: These builds can still run on AMD processors, but they're statically linked to Intel MKL, so some linear algebra operations will be slow. 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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