2 September: –dose ‘noheader’ is today work properly whenever specific phenotypes is destroyed. –vcf + –vcf-filter out today parses semicolon-delimited Filter fields correctly. –vcf-min-gq banner added to advancement build. –exclude/–extract don’t keeps awful show when the main dataset additionally the –exclude/–pull variation listing features scores of ‘.’ records.
28 August: –recode HV[-1chr] now always spends ‘0’ given that destroyed phenotype password, because Haploview does not take on -nine. –write-covar + –with-phenotype not any longer segfaults into circumstances/control phenotypes, and multichar allele .ped loader no further segfaults into the nonstandard tri/quadallelic variants. –meta-data put in creativity make.
14 August: Fixed a beneficial typo regarding eleven August make and this triggered covariate loading and a few almost every other attributes to hang.
11 August: –linear/–logistic no more uses a push chair Huber-White fundamental mistake estimator whenever clusters try outlined. –output-chr today work securely with –make-sleep in the event the input .bim is actually unsorted, and you will a long allele code inside the an unsorted .bim no more factors –make-bed in order to segfault.
1 August: –amount logistic regression bugfix. –make-just-bim and you can –make-just-fam flags extra. .bim/.fam files can now be processed in place of an accompanying .bed less than particular products. –recode-allele now work securely having An effective-transpose setting.
18 July: Text filesets with one another multi-character allele codes and you may an unsorted .map document no further cause the autoconverter so you can freeze. –pfilter is now constantly filter out ‘NA’ records. –dose chromosome code productivity bug repaired. –read-freq now loads A1 allele codes when they are destroyed on the chief dataset, rather than erroring call at one to condition. –show-tags put in development create.
Basic Cochran-Mantel-Haenszel and you will Breslow-Day assessment placed into invention create
4 July: Repaired a couple of mix insects and this possibly triggered research during the last couple examples of a feedback or combined fileset getting mishandled. 90 leader/beta builds, and most a couple of products was indeed with it, we strongly recommend redoing the newest combine with a newer make. (Extremely merges was indeed unaffected, however, top secure than sorry.)
When you have matched filesets generated with earlier PLINK step 1
step 1 July: Improve recently put (sorry about that) –data/–gen/–shot order-range parsing insect. –indep no more misreports just how many pruned alternatives when indeed there is actually extensive multicollinearity. –fst, –homog, and –oxford-pheno-identity flags added.
27 June: “–recode oxford” not dumps incorrect IDs whenever used in an equivalent work at just like the an example filter out. –fill-missing-a2 flag additional. –recode ‘A-transpose’ and you will ‘include-alt’ modifiers extra. “–het quick-sample” form extra.
20 June: Fixed –mendel zero chromosome password/segfault insect. –merge-record no longer means a guide fileset. –fast-epistasis + –synchronous bugfix. –indep-pairphase and you will QFAM take to completed in advancement create.
10 Summer: –merge-form step one now accurately merges lost phone regole incontri lesbiche calls with just one nonmissing telephone call. –r/–r2 chromosome border addressing bugfixes. ‘0X’/’0Y’/’0M’ chromosome rules produced from the Oxford units are in fact accepted, and have now backed by –output-chr. –vcf-half-label flag placed into govern management of ‘0/.’ VCF GT beliefs, and you can default behavior happens to be ‘error’ form to force an aware ent build.
5 June: –ld-snp-record and you can multipass –r/–r2 bugfixes. Nonstandard ‘0/.’ and you can similar VCF GT job beliefs are actually canned given that whenever they didn’t have the fresh behind ‘/.’, instead of causing good segfault. (Handling of this example is configurable afterwards, stay tuned.) –linear/–logistic permutation bugfix (permutation profits number range wasn’t initialized to all the-zero). –serving linear regression placed into creativity create.
3 Summer: Gzipper not deletes the fresh production document when getting expected to help you append (it was ultimately causing big n-admission computations such –r2 gz to simply support the output of your own last citation). Repaired –genome double-missing-call handling bug, and you will a good –r/–r2 blended autosomal/nonautosomal data-handling bug. “–serving exist” and you can –write-amount placed into creativity generate.
e-related segfaults. “–r2 dprime” missing data handling bugfix. Corrected misnamed –filter-attrib[-indiv] flags to –attrib[-indiv], fixed a positive matching bug, and added support for gzipped attribute files. “–recode tab” not any longer gives off rooms in the header range. –blocks is now offering an effective ‘no-pheno-req’ modifier which removes the unnecessary phenotype requirements. –annotate put in development create.