twenty six March: “–recode vcf” heading modified to possess being compatible with VCFtoolspact 1000 Genomes stage step 1 study data files printed into tips webpage.
Single-precision binary matrix yields (elizabeth
dos February: –bcf now covers BCFv2.2 nonzero missing genotype and you can prevent-of-vector thinking (produced by elizabeth.g. bcftools 1.1) safely. –mendel-multigen has stopped being prohibited by the command-line parser whenever a family-depending relationship try try work on. –destroyed, –freq, –hardy, and you may –het today support gzipped productivity (add the ‘gz’ modifier). –Roentgen put in advancement generate.
fifteen January: –keep/–beat now really works properly on recently-updated IDs when –update-ids is within the exact same manage. –mac/–max-mac added to innovation create.
twelve January: –dosage + –covar + –intercourse now works properly, and you will a wrong alerting regarding PLINK step 1.07 execution might have been eliminated. –dose logistic regression not any longer profile incorrect p-values for very small samples.
(beta 3): –epistasis implemented, with heavy optimization for quantitative traits. “–recode vcf< ,-fid,-iid>” now flags reference alleles as “possibly not based on a real reference genome” unless –real-ref-alleles is also specified, and sets ALT alleles to ‘.’ when they are not present in the immediate dataset. –vcf-min-gq and –vcf-min-gp no longer error out when a genotype entry has fewer fields than expected, since the VCF specification explicitly states that this is an acceptable way to represent trailing missing values. –make-bed no longer segfaults when resorting a file too large to fit in memory. Lees verder