13 Get: –logistic + gender covariate bugfix. –snp instead –windows no more behaves eg –snp + “–window 0” when most other variations display an identical bp complement. –pca today errors out in place of going back all-zero eigenvalues/vectors when examples with no genotype studies can be found.
11 Could possibly get (beta 1): Fast third-team –logistic code provided (get a hold of credit webpage to possess facts). –output-chr additional. –family relations and you may –make-perm-pheno implemented. Within-group permutation bugfix. –linear/–logistic dominant/recessive activities and covariate affairs work now. –testing bugfix.
15 April: –bcf today contributes step 1 to variant coordinates, as the its coordinates is discussed become 0-depending when you find yourself VCF is actually step 1-mainly based.
fourteen April: –check-sex/–impute-gender not silently takes into account nonmissing Y genotype counts by default. –bcf today snacks shed variant IDs because if they certainly were equal in order to ‘.’, as opposed to erroring out.
8 April: Centimorgan condition loading bugfix. –mendel error breakdown format bugfix. –lambda bugfix. –to alter now designs and you can logs estimated genomic control lambda really worth. –keep[-fam]/–remove[-fam] enter in data files having content IDs today just trigger a warning as an alternative out of a blunder. –check-sex/–impute-gender now has a good ‘y-only’ setting.
5 April: –not-chr bugfix. https://datingranking.net/fr/brancher/ “–recode fastphase” no further non-payments to 0/1 allele codes (although they may be able be requested that have age.grams. “–recode 01 fastphase”). –hardy2/–hwe2 now invoke the new mid-p modified designs off –hardy and you can –hwe, so you can reflect the initial chi-square test’s lack of traditional prejudice.
Very first mother or father-of-provider shot then followed
es and marker IDs to help you really be matched on situation/manage investigation. –check-sex/–impute-gender now explore Y chromosome analysis when it is introduce. –flip-subset, –flip-always check, and you can very first perfect binomial try –tdt then followed.
28 March: Repaired –bcf bug one to brought about it to help you fail assuming there have been numerous Structure sphere. –rating forgotten phenotype productivity bugfix.
twenty-seven February: Fixed –bcf heading range parsing insect (loading should not any longer falter if the GT heading line appears once a low-Solution Information otherwise Filter out range, and you will –vcf-filter should today work with BCF2 data files). –split-x ‘hg20’ create password corrected in order to ‘hg38’. –ibc Fhat2/Fhat3 bugfix. –het and you will –set-me-forgotten adopted.
26 March: –hardy/–hwe X chromosome case/handle bugfix. –extract/–prohibit now considers every token in a file, rather than the first on each range (this is undocumented PLINK step 1.07 decisions).
twenty-five February: –bcf not does not load new bcftools-made files which have ‘IDX=’ with the the end of the fresh GT meta-suggestions range. Document transfer shortcuts (–vcf + –away versus –make-sleep, etc.) today error aside whenever a filter flag one to wouldn’t take effect (elizabeth.g. –pull, –hwe, –snps-just. ) are given. –me and you may –mendel followed; –mendel-duos and you may –mendel-multigen flags put into extend the capability. Fixed PLINK step 1.07 –mendel question where genotypes could be set-to shed prior to browsing is actually over (we.elizabeth. in the event the there have been overlapping trios, PLINK step 1.07 you will don’t report particular problems).
20 February: –condition-checklist command range parsing bugfix, –recode beagle bugfix, –make-creators bugfix, test filtering bugfix to have –regress-range and you may –recode lgen/list/rlist. First –get implemention.
Ueki/Cordell mutual-consequences shot today skips marker sets having less than 5 findings in almost any contingency table telephone (where instances and control are believed separately); so it tolerance is actually changeable which have –je-cellmin
fifteen February: Several approaches to the latest haplotype volume cubic equation (which arises whenever researching Lewontin’s D-prime) will be now often be handled precisely; there are a number of part cases which have been mishandled just before. Indicators with similar bp coordinates not end up in step 1.9 –stops so you’re able to give various other abilities than just step one.07 –stops.
14 March: –prevents adopted. D-finest data (“–r2 dprime”, –ld, –reduces, –clump) of versions toward X chromosome now rightly downweight people relative so you’re able to lady. –vcf and you can –bcf today manage take to ID rooms in the a good trends.
eight February: Fixed small –genome bug you to definitely slash Z2 imagine so you’re able to 0 in place of step one when it try too large. –all-pheno and you can –loop-assoc now print case/handle matters for every single phenotype.
