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. But when you used the UNAFF rows throughout the –sturdy declaration getting something, you ought to rerun –sturdy on current create. ) set-attempt numerous-assessment correction today counts nonempty kits having zero tall variations.
7 December: –to evolve today applies to the latest combined take to fact instead of the additive feeling when the previous is actually calculated, no offered accounts linearly genomic-managed p-thinking after they would be invalid. Some numeric balances improvements for quick p-thinking. –logistic permutation make sure –assoc/–design lay-sample bugfixes. –linear/–logistic place-test and –amount ‘sex’ modifier accompanied. –amount + –gender error content now explains one PLINK 1.07 didn’t manage that it flag integration properly.
twenty-five November: Repaired –exclude/–pull recollections management bug in 2 November create. –get now supporting dosage studies. –write-amount no more produces wrong IDs whenever attempt filter systems is used. –serving ‘noheader’ can be used that have ‘list’ when each group only has you to definitely file. –assoc/–design set-decide to try then followed. –set-missing-var-ids prolonged to permit introduction of allele labels, and –set-missing-snp-ids/–set-missing-nonsnp-ids resigned. UNADJ line values are now right when you look at the “–to evolve gc” records.
dos November: Improved variant ID research rates. g. –make-grm-bin) is actually considering twice-precision interior calculations, as well as the ‘bin’ + ‘single-prec’ modifier integration has been replaced with ‘bin4’.
15 October: Repaired an insect from inside the –vcf’s handling of variants with ten or even more approach alleles. –serving Zout not any longer segfaults at the bottom. Merger no longer scrambles centimorgan coordinates.
20 Sep: Repaired non-tight –biallelic-just insect when dealing with multiallelic versions. For those who have made use of –biallelic-just instead ‘strict’ with the VCF data files with triallelic variants, we strongly recommend rerunning the fresh operation on newest make. Fixed decimal trait –assoc insect you to caused they to type for each output line double, and –linear/–logistic mishandling of some datasets having heterozygous haploid phone calls. –vcf-min-gp added to advancement make.
18 Sep: –no-fid bugfix. Visibility regarding nonnumeric phenotype chain (e.g. ‘NA’) don’t push the phenotype are managed once the decimal. –output-missing-phenotype today accepts nonnumeric strings. “–dosage list” now works properly with several batches. –oxford-single-chr banner put into allow it to be loading regarding single-chromosome .gen files that have ignorable SNP ID profession thinking. –genome not doesn’t statement some parent-little ones relationship. –update-alleles was still forgotten a few matches of forgotten genotypes; this has been repaired.