twenty six February: “–recode vcf” header changed for compatibility with VCFtoolspact one thousand Genomes stage step one studies data released into the resources page.
Single-accuracy binary matrix production (age
2 February: –bcf now handles BCFv2.dos nonzero shed genotype and you can prevent-of-vector beliefs (emitted by the age.g. bcftools step one.1) properly. –mendel-multigen is no longer blocked by demand-line parser when a household-oriented connection sample is work with. –lost, –freq, –sturdy, and you can –het today help gzipped production (are the ‘gz’ modifier). –R set in innovation build.
15 January: –keep/–eliminate now performs safely to your newly-upgraded IDs whenever –update-ids is within the exact same run. –mac/–max-mac added to advancement make.
twelve January: –dosage + –covar + –gender today really works securely, and you will an incorrect warning towards PLINK step one.07 execution might have been got rid of. –serving logistic regression not any longer accounts poor p-values to possess very small examples.
(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 https://datingranking.net/es/fechado/ resorting a file too large to fit in memory. Continue reading “Oxford-style transfer now tolerates the same A1/A2 allele requirements”