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.
: –dummy, –show-labels, –neighbor, –mh/–bd/–mh2/–homog and you will –clump-profession bugfixes. –q-score-diversity implemented for dose research. –split-x/–merge-x ‘no-fail’ modifier placed into support data conversion programs.
Digital –length production bugfix
13 December: Case/control –hardy/–hwe no further at random excludes so many controls out-of control-only stage out-of try. (This is generally simple, as the the-products attempt nevertheless has worked, as well as the bug was only browsing occur when –hardy/–hwe was a student in the same focus on due to the fact most other strain such –exclude/–extract. But if you used the UNAFF rows on the –robust report to own one thing, you need to rerun –robust to your latest make. ) set-shot multiple-comparison modification today counts nonempty kits with no significant versions.
seven December: –to change now pertains to the brand new combined take to fact rather than the ingredient impression in the event that previous try computed, with no prolonged account linearly genomic-regulated p-thinking when they could be invalid. Some numeric balance improvements to own quick p-philosophy. –logistic permutation test and –assoc/–design place-shot bugfixes. –linear/–logistic place-ensure that you –amount ‘sex’ modifier observed. –dose + –sex mistake content now demonstrates to you that PLINK step one.07 did not handle it flag consolidation safely.
twenty-five November: Repaired –exclude/–extract memory government insect in 2 November create. –rating today supporting dose investigation. –write-amount not writes wrong IDs whenever decide to try strain is applied. –dosage ‘noheader’ is now able to be studied having ‘list’ when for every group has only one to document. –assoc/–design set-decide to https://datingranking.net/de/bhm-dating-de/ try used. –set-missing-var-ids stretched permitting inclusion from allele names, and –set-missing-snp-ids/–set-missing-nonsnp-ids resigned. UNADJ line philosophy are actually correct when you look at the “–to alter gc” records.
2 November: Increased version ID look rate. grams. –make-grm-bin) grew to become according to twice-reliability inner data, and ‘bin’ + ‘single-prec’ modifier combination might have been substituted for ‘bin4’.
fifteen October: Repaired a bug during the –vcf’s management of versions with 10 or even more option alleles. –dosage Zout no longer segfaults at the end. Merger not any longer scrambles centimorgan coordinates.
20 September: Repaired low-tight –biallelic-only bug when approaching multiallelic variants. When you have utilized –biallelic-simply as opposed to ‘strict’ toward VCF data files which have triallelic variants, i strongly recommend rerunning the fresh new process toward most recent build. Repaired decimal characteristic –assoc insect that caused it to type for every single efficiency range twice, and –linear/–logistic mishandling of some datasets with heterozygous haploid phone calls. –vcf-min-gp put in advancement create.
18 September: –no-fid bugfix. Visibility regarding nonnumeric phenotype strings (age.grams. ‘NA’) don’t force the brand new phenotype becoming managed due to the fact decimal. –output-missing-phenotype today welcomes nonnumeric strings. “–dose listing” now really works securely which have multiple batches. –oxford-single-chr banner put into succeed packing of single-chromosome .gen data files which have ignorable SNP ID job thinking. –genome don’t fails to report specific mother or father-children dating. –update-alleles had been lost several suits involving destroyed genotypes; it’s been fixed.