thirteen Will get: –logistic + gender covariate bugfix. –snp instead of –screen don’t behaves such as for instance –snp + “–screen 0” whenever most other alternatives display a similar bp coordinate. –pca now mistakes away in the place of coming back most of the-zero eigenvalues/vectors when trials and no genotype research exists.
eleven Can get (beta 1): Timely third-class –logistic password provided (see loans webpage getting facts). –output-chr extra. –family members and you may –make-perm-pheno observed. Within-class permutation bugfix. –linear/–logistic prominent/recessive designs and you can covariate interactions functions today. –testing bugfix.
15 April: –bcf now adds 1 to variation coordinates, once the their coordinates was defined are 0-situated whenever you are VCF is actually step 1-established.
14 April: –check-sex/–impute-gender don’t silently takes into account nonmissing Y genotype counts automagically. –bcf today snacks missing variation IDs since if they certainly were equivalent to help you ‘.’, unlike erroring away.
8 April: Centimorgan standing loading bugfix. –mendel mistake description formatting bugfix. –lambda bugfix. –to alter today prints and you will logs estimated genomic control lambda value. –keep[-fam]/–remove[-fam] enter in records with duplicate IDs today only lead to a caution as an alternative regarding a blunder. –check-sex/–impute-gender presently has good ‘y-only’ form.
5 April: –not-chr bugfix. “–recode fastphase” don’t defaults in order to 0/step 1 allele requirements (even when they’re able to still be requested which have age.g. “–recode 01 fastphase”). –hardy2/–hwe2 now invoke new middle-p modified designs away from –sturdy and you can –hwe, in order to echo the original chi-rectangular test’s diminished traditional bias.
Very first moms and dad-of-resource attempt adopted
es and you will marker IDs so you can be merged towards instance/manage study. –check-sex/–impute-intercourse today use Y chromosome study when it is introduce. –flip-subset, –flip-see, and first exact binomial attempt –tdt observed.
twenty eight February: Repaired –bcf insect you to definitely triggered it to falter while there have been several Format areas. –rating shed phenotype output bugfix.
twenty seven March: Repaired –bcf heading range parsing insect (packing is not falter if GT header range appears after a non-Citation Information otherwise Filter range, and you can –vcf-filter should now work with BCF2 files). –split-x ‘hg20’ generate code corrected to ‘hg38’. –ibc Fhat2/Fhat3 bugfix. –het and you will –set-me-forgotten observed.
twenty six February: –hardy/–hwe X-chromosome circumstances/manage bugfix. –extract/–exclude today considers every token during the a document, instead of just the original on each line (it was undocumented PLINK step one.07 choices).
twenty-five February: –bcf not doesn’t stream brand new bcftools-produced data which have ‘IDX=’ toward the end of the newest GT meta-pointers line. Document import shortcuts (–vcf + –out without –make-bed, etcetera.) now error away when a filter flag that wouldn’t begin working (age.g. –pull, –hwe, –snps-simply. ) was given. –me and you can –mendel followed; –mendel-duos and you will –mendel-multigen flags put in expand the abilities. Fixed PLINK step one.07 –mendel material in which genotypes could be set-to shed ahead of studying is actually done (i.age. if the there have been overlapping trios, PLINK 1.07 you can expect to don’t declaration some mistakes).
20 February: –condition-record order range parsing bugfix, –recode beagle bugfix, –make-founders bugfix, test filtering bugfix to possess –regress-point and you may –recode lgen/list/rlist. First –score implemention.
Ueki/Cordell combined-consequences sample now skips marker sets which have less than 5 observations in any backup table cellphone (in which instances and you can controls are considered alone); this tolerance is varying which have –je-cellmin
fifteen February: Numerous solutions to the newest haplotype regularity cubic formula (and therefore arises whenever comparing Lewontin’s D-prime) is to today often be handled correctly; there have been a few part cases that have been mishandled in advance of. Markers that have the same bp coordinates no more trigger step 1.nine –blocks so you’re able to yield more abilities than step 1.07 –stops.
14 February: –blocks observed. sitios de citas budistas D-perfect data (“–r2 dprime”, –ld, –reduces, –clump) connected with alternatives into the X-chromosome today rightly downweight guys cousin to help you women. –vcf and you can –bcf today deal with sample ID spaces in the a fair manner.
eight March: Repaired lesser –genome bug that clipped Z2 guess to 0 rather than 1 if this was too big. –all-pheno and you will –loop-assoc today print situation/handle counts for every phenotype.