13 May: –logistic + intercourse covariate bugfix. –snp instead –screen no longer behaves such as for example –snp + «–window 0» when most other versions display the same bp coordinate. –pca now mistakes away in the place of coming back most of the-zero eigenvalues/vectors whenever samples with no genotype investigation can be https://datingranking.net/fr/evaluez-ma-date/ found.
eleven Will get (beta step 1): Quick third-team –logistic password integrated (pick loans webpage to own info). –output-chr extra. –loved ones and –make-perm-pheno implemented. Within-class permutation bugfix. –linear/–logistic principal/recessive designs and you will covariate relations works now. –screening bugfix.
15 April: –bcf today adds step one to variation coordinates, as the their coordinates are defined is 0-created whenever you are VCF are step 1-depending.
fourteen April: –check-sex/–impute-gender not any longer silently considers nonmissing Y genotype counts automatically. –bcf now snacks forgotten version IDs as if they were equal so you’re able to ‘.’, as opposed to erroring out.
8 April: Centimorgan updates packing bugfix. –mendel error breakdown format bugfix. –lambda bugfix. –to alter today designs and you will logs projected genomic control lambda well worth. –keep[-fam]/–remove[-fam] input data files that have duplicate IDs today simply produce an alert instead out-of a mistake. –check-sex/–impute-sex is now offering a great ‘y-only’ mode.
5 April: –not-chr bugfix. «–recode fastphase» not non-payments to 0/step one allele rules (regardless if they are able to remain questioned having elizabeth.g. «–recode 01 fastphase»). –hardy2/–hwe2 now invoke this new mid-p adjusted models out of –sturdy and you will –hwe, in order to reflect the original chi-rectangular test’s not enough conservative prejudice.
es and you will marker IDs to sometimes be matched towards circumstances/manage study. –check-sex/–impute-intercourse today explore Y chromosome study when it’s expose. –flip-subset, –flip-always check, and you may first direct binomial attempt –tdt then followed.
28 February: Repaired –bcf bug you to definitely triggered it so you’re able to fail and if there are multiple Format industries. –score lost phenotype efficiency bugfix.
27 February: Repaired –bcf heading range parsing insect (packing is no further falter when the GT heading line looks after a non-Ticket Info or Filter range, and you will –vcf-filter out is to today manage BCF2 data files). –split-x ‘hg20’ create password corrected in order to ‘hg38’. –ibc Fhat2/Fhat3 bugfix. –het and you may –set-me-missing implemented.
26 March: –hardy/–hwe X-chromosome case/control bugfix. –extract/–prohibit today takes into account all of the token in the a document, rather than just the initial on every line (this was undocumented PLINK 1.07 decisions).
twenty five February: –bcf no more fails to stream brand-new bcftools-produced files having ‘IDX=’ into the the conclusion new GT meta-recommendations range. File import shortcuts (–vcf + –out instead of –make-bed, etc.) now mistake away whenever a filter flag one to would not begin working (age.grams. –extract, –hwe, –snps-merely. ) are given. –me personally and you can –mendel implemented; –mendel-duos and you can –mendel-multigen flags placed into increase their possibilities. Fixed PLINK step 1.07 –mendel question where genotypes would-be set to missing before browsing is over (we.elizabeth. if the there have been overlapping trios, PLINK step 1.07 you may neglect to report specific problems).
20 March: –condition-record demand range parsing bugfix, –recode beagle bugfix, –make-founders bugfix, try selection bugfix for –regress-range and you will –recode lgen/list/rlist. Very first –get implemention.
15 February: Several remedies for the fresh new haplotype regularity cubic picture (which arises whenever researching Lewontin’s D-prime) will be now often be addressed precisely; there have been a few place times that have been mishandled in advance of. Markers having similar bp coordinates don’t cause step 1.9 –reduces to help you yield other show than just step one.07 –reduces.
fourteen March: –stops observed. D-prime calculations («–r2 dprime», –ld, –blocks, –clump) of alternatives on X-chromosome today appropriately downweight guys cousin to girls. –vcf and you can –bcf today deal with shot ID rooms in a fair trends.
seven February: Repaired slight –genome bug one reduce Z2 guess in order to 0 in place of 1 whether it are too large. –all-pheno and you may –loop-assoc now print circumstances/handle counts for each and every phenotype.
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