twenty-six February: “–recode vcf” header altered to have compatibility that have VCFtoolspact a thousand Genomes stage 1 data data files released towards the tips web page.
Single-accuracy binary matrix returns (e
2 March: –bcf today handles BCFv2.dos nonzero missing genotype and avoid-of-vector philosophy (released by the e.grams. bcftools step one.1) properly. –mendel-multigen is no longer prohibited by the order-range parser whenever a household-oriented organization shot was work with. –shed, –freq, –sturdy, and you can –het now support gzipped production (add the ‘gz’ modifier). –R added to creativity build.
15 January: –keep/–reduce now functions properly on the freshly-upgraded IDs when –update-ids is within the exact same focus on. –mac/–max-mac set in advancement make.
12 January: –serving + –covar + –intercourse now really works safely, and an incorrect warning in regards to the PLINK step one.07 implementation might have been got rid of. –serving logistic regression no longer records inappropriate p-viewpoints to have 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 http://datingranking.net/de/behinderte-dating 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.
: –dummy, –show-labels, –neighbor, –mh/–bd/–mh2/–homog and you may –clump-industry bugfixes. –q-score-assortment accompanied for dose data. –split-x/–merge-x ‘no-fail’ modifier added to help study transformation programs.
Binary –length productivity bugfix
13 December: Case/handle –hardy/–hwe no more randomly excludes too many controls off control-just phase of try. (This is mainly simple, once the all the-trials attempt nevertheless has worked, plus the bug was just probably are present when –hardy/–hwe was at a similar work with because the almost every other filter systems including –exclude/–extract. Continue reading Oxford-format transfer today tolerates similar A1/A2 allele requirements