Logging now permits gPLINK so you can constantly place production records


Logging now permits gPLINK so you can constantly place production records

thirteen May: –logistic + sex covariate bugfix. –snp versus –window don’t acts such as for example –snp + “–windows 0” when most other versions share a comparable bp accentuate. –pca today errors aside instead of coming back the-no eigenvalues/vectors when trials and no genotype study occur.

eleven Could possibly get (beta step 1): Quick 3rd-team –logistic password incorporated (come across loans webpage to own details). –output-chr extra. –family relations and –make-perm-pheno accompanied. Within-cluster permutation bugfix. –linear/–logistic prominent/recessive activities and you may covariate affairs performs today. –testing bugfix.

fifteen April: http://www.datingranking.net/de/dating-in-ihren-40ern –bcf now adds 1 to help you version coordinates, due to the fact the coordinates is defined getting 0-situated if you find yourself VCF is step 1-situated.

14 April: –check-sex/–impute-sex no more silently takes into account nonmissing Y genotype counts automatically. –bcf today snacks missing variant IDs as if these people were equal to help you ‘.’, in lieu of erroring away.

8 April: Centimorgan position packing bugfix. –mendel error description formatting bugfix. –lambda bugfix. –adjust now prints and you may logs projected genomic control lambda really worth. –keep[-fam]/–remove[-fam] enter in files with copy IDs now merely end in an alert rather off an error. –check-sex/–impute-intercourse is now offering good ‘y-only’ means.

5 April: –not-chr bugfix. “–recode fastphase” no more non-payments to help you 0/1 allele codes (though they are able to nevertheless be requested which have age.grams. “–recode 01 fastphase”). –hardy2/–hwe2 now invoke the mid-p modified brands out-of –hardy and you can –hwe, to help you echo the initial chi-rectangular test’s diminished conventional prejudice.

Earliest father or mother-of-provider attempt followed

es and marker IDs so you can really be combined for the instance/handle studies. –check-sex/–impute-gender today use Y chromosome studies when it’s establish. –flip-subset, –flip-inspect, and very first right binomial take to –tdt used.

28 March: Fixed –bcf bug you to caused it in order to falter of course, if there were numerous Structure sphere. –get shed phenotype yields bugfix.

twenty seven February: Repaired –bcf header line parsing bug (packing should no longer falter in the event that GT header range appears just after a non-Citation Information or Filter range, and you can –vcf-filter out will be today focus on BCF2 files). –split-x ‘hg20’ build code corrected so you’re able to ‘hg38’. –ibc Fhat2/Fhat3 bugfix. –het and you may –set-me-missing adopted.

twenty six February: –hardy/–hwe X-chromosome circumstances/manage bugfix. –extract/–prohibit now takes into account all the token from inside the a file, rather than the initial for each range (it was undocumented PLINK step 1.07 behavior).

25 February: –bcf don’t fails to load brand new bcftools-produced data files which have ‘IDX=’ towards the end of the GT meta-suggestions line. Document import shortcuts (–vcf + –away rather than –make-bed, etcetera.) now mistake out whenever a filtration flag you to would not take effect (elizabeth.g. –pull, –hwe, –snps-just. ) was specified. –me and you will –mendel adopted; –mendel-duos and you can –mendel-multigen flags put into stretch their capability. Fixed PLINK step 1.07 –mendel topic where genotypes was set-to lost just before checking is actually complete (we.age. in the event that there were overlapping trios, PLINK step 1.07 you will definitely are not able to statement specific problems).

20 February: –condition-checklist order range parsing bugfix, –recode beagle bugfix, –make-founders bugfix, attempt selection bugfix getting –regress-range and you can –recode lgen/list/rlist. First –rating implemention.

Ueki/Cordell shared-effects test today skips marker sets with less than 5 findings in any backup table mobile (where instances and you will regulation are considered individually); which tolerance was changeable with –je-cellmin

fifteen February: Numerous ways to this new haplotype frequency cubic formula (and this comes up when evaluating Lewontin’s D-prime) is always to now continually be handled truthfully; there had been a few spot cases that have been mishandled ahead of. Indicators which have similar bp coordinates no further bring about step one.nine –stops so you’re able to give other performance than step 1.07 –prevents.

14 March: –blocks used. D-perfect computations (“–r2 dprime”, –ld, –reduces, –clump) involving versions on the X-chromosome today rightly downweight boys relative so you can female. –vcf and you can –bcf today manage test ID areas from inside the a reasonable trends.

eight March: Repaired slight –genome bug you to clipped Z2 guess in order to 0 unlike 1 if it is too big. –all-pheno and –loop-assoc now printing instance/control matters each phenotype.


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