twenty six March: “–recode vcf” header modified getting compatibility with VCFtoolspact a thousand Genomes phase 1 study records posted toward information webpage.
Single-reliability binary matrix productivity (elizabeth
2 March: –bcf today covers BCFv2.2 nonzero lost genotype and you may prevent-of-vector values (released by the age.g. bcftools 1.1) safely. –mendel-multigen no longer is blocked of the command-range parser whenever a family-oriented association try is focus on. –shed, –freq, –sturdy, and you can –het now help gzipped output (are the ‘gz’ modifier). –R placed into innovation build.
15 January: –keep/–dump today really works securely toward recently-current IDs whenever –update-ids is in the exact same work with. –mac/–max-mac computer put into creativity create.
twelve January: –serving + –covar + –intercourse today works securely, and you may an inaccurate warning concerning the PLINK step one.07 execution could have been eliminated. –serving logistic regression not any longer account poor p-opinions to own very small trials.
(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.
: –dummy, –show-tags, –neighbor, –mh/–bd/–mh2/–homog and you will –clump-career bugfixes. –q-score-variety implemented to possess amount investigation. –split-x/–merge-x ‘no-fail’ modifier put into assistance investigation conversion programs.
Digital –distance yields bugfix
thirteen December: Case/manage –hardy/–hwe no further randomly excludes unnecessary regulation out-of manage-just phase out-of take to. (This was primarily harmless, once the all-products decide to try however spent some time working, as well as the bug was only attending exists when –hardy/–hwe was in a similar work with once the other strain such as –exclude/–pull. But when you made use of the UNAFF rows in the –hardy declaration to possess something, you need to rerun –robust towards latest create. ) set-decide to try multiple-evaluation correction now counts nonempty set that have no extreme variations.
7 December: –adjust now relates to the newest combined sample figure rather than the ingredient impression in the event that previous is actually determined, and no offered reports linearly genomic-managed p-values when they will be incorrect. Particular numeric balances improvements to have small p-thinking. –logistic permutation make sure –assoc/–design set-shot bugfixes. –linear/–logistic set-ensure that you –dosage ‘sex’ modifier implemented. –serving + –intercourse mistake content now demonstrates to you you to definitely PLINK 1.07 did not deal with that it banner combination securely.
25 November: Repaired –exclude/–pull thoughts administration bug in 2 November build. –rating now helps amount data. –write-amount no longer writes completely wrong IDs whenever take to filter systems is actually used. –dose ‘noheader’ can be used with ‘list’ whenever per group only has that file. –assoc/–design place-test used. –set-missing-var-ids prolonged to http://www.datingranking.net/de/anschliesen permit addition away from allele brands, and you may –set-missing-snp-ids/–set-missing-nonsnp-ids retired. UNADJ column viewpoints are in fact proper inside the “–to evolve gc” accounts.
2 November: Increased variation ID search price. grams. –make-grm-bin) has grown to become centered on double-reliability inner calculations, as well as the ‘bin’ + ‘single-prec’ modifier integration might have been replaced with ‘bin4’.
15 October: Fixed a pest when you look at the –vcf’s management of variants with ten or maybe more option alleles. –serving Zout don’t segfaults in the bottom. Merger no further scrambles centimorgan coordinates.
20 September: Fixed low-strict –biallelic-simply insect when approaching multiallelic variations. If you have made use of –biallelic-simply versus ‘strict’ on VCF documents which have triallelic alternatives, we suggest rerunning the procedure into latest create. Fixed quantitative attribute –assoc insect you to triggered they to write for each returns line twice, and you may –linear/–logistic mishandling of a few datasets having heterozygous haploid phone calls. –vcf-min-gp set in development create.
18 September: –no-fid bugfix. Presence regarding nonnumeric phenotype chain (age.grams. ‘NA’) no longer push this new phenotype as managed since decimal. –output-missing-phenotype today allows nonnumeric chain. “–dosage number” today performs securely which have several batches. –oxford-single-chr banner placed into allow packing out-of unmarried-chromosome .gen files having ignorable SNP ID job viewpoints. –genome not any longer doesn’t declaration some father or mother-youngsters matchmaking. –update-alleles was still shed several suits of forgotten genotypes; it has been repaired.