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Oxford-style transfer now tolerates the same A1/A2 allele codes

Oxford-style transfer now tolerates the same A1/A2 allele codes

twenty six February: “–recode vcf” heading changed having compatibility which have VCFtoolspact a lot of Genomes stage 1 research files printed for the info page.

Single-reliability digital matrix efficiency (e

dos March: –bcf today handles BCFv2.2 nonzero forgotten genotype and you may avoid-of-vector viewpoints (released from the age.grams. bcftools 1.1) safely. –mendel-multigen is no longer blocked of the demand-range parser when a family-established organization test are work with. –destroyed, –freq, –robust, and you may –het now service gzipped productivity (range from the ‘gz’ modifier). –R placed into innovation build.

fifteen January: –keep/–cure today really works securely to the recently-up-to-date IDs whenever –update-ids is in the exact same manage. –mac/–max-mac set in invention generate.

a dozen January: –amount + –covar + –sex today work safely, and you may an inaccurate alerting in regards to the PLINK step one.07 execution has been eliminated. –dosage logistic regression not any longer profile poor p-values to have very small samples.

(beta 3): –epistasis implemented, with heavy optimization for quantitative traits. “–recode vcf<,-fid,-iid>” now flags reference alleles as “possibly not based on a real reference genome” unless –real-ref-alleles is also specified, and sets ALT alleles to ‘.’ when they are not present in the immediate dataset. –vcf-min-gq and –vcf-min-gp no longer error out when a genotype entry has fewer fields than expected, since the VCF specification explicitly states that this is an acceptable way to represent trailing missing values. –make-bed no longer segfaults when resorting a file too large to fit in memory.

: –dummy, –show-tags, –neighbour, –mh/–bd/–mh2/–homog and –clump-profession bugfixes. –q-score-diversity used having serving research. –split-x/–merge-x ‘no-fail’ modifier added to assistance investigation sales scripts.

Digital –length yields bugfix

13 December: Case/handle –hardy/–hwe don’t randomly excludes a lot of controls off control-only stage away from try. (It was mostly innocuous, as all the-examples decide to try nevertheless has worked, and the bug was only gonna exist when –hardy/–hwe was in the same run because the most other strain such –exclude/–extract. But when you made use of the UNAFF rows in the –hardy declaration to have one thing, you should rerun –hardy into the newest generate. ) set-shot several-testing modification today matters nonempty kits with no tall versions.

eight December: –to alter today pertains to the brand new shared test figure rather than the additive perception in the event that former was determined, and no longer account linearly genomic-managed p-beliefs once they was incorrect. Particular numeric balances improvements getting brief p-values. –logistic permutation ensure that you –assoc/–design put-sample bugfixes. –linear/–logistic place-make sure –amount ‘sex’ modifier then followed. –serving + –gender mistake content now shows you you to definitely PLINK 1.07 did not handle this flag integration securely.

twenty-five November: Fixed –exclude/–extract memories management insect in two November generate. –rating now supports dose studies. –write-serving not any longer writes incorrect IDs when shot filters is applied. –amount ‘noheader’ is now able to be studied that have ‘list’ when per batch has only that document. –assoc/–design set-decide to try accompanied. –set-missing-var-ids stretched allowing introduction from allele labels, and –set-missing-snp-ids/–set-missing-nonsnp-ids resigned. UNADJ line philosophy are now actually correct for the “–to improve gc” profile.

2 November: Increased variation ID lookup speed. grams. –make-grm-bin) has started to become based on twice-accuracy internal computations, and also the ‘bin’ + ‘single-prec’ modifier combination might have been replaced with ‘bin4’.

15 Oct: Fixed a bug in –vcf’s management of versions which have 10 or more option alleles. –dosage Zout no further segfaults in the bottom. Merger don’t scrambles centimorgan coordinates.

20 Sep: Repaired low-tight –biallelic-merely bug whenever addressing multiallelic variants. If you have made use of –biallelic-just versus ‘strict’ on VCF records having triallelic variants, i recommend rerunning this new process with the newest make. Fixed decimal feature –assoc insect one caused it to type for every single production range double, and you may –linear/–logistic mishandling of some datasets having heterozygous haploid calls. –vcf-min-gp placed into creativity build.

18 September: –no-fid bugfix. Exposure out-of nonnumeric phenotype chain (elizabeth.grams. ‘NA’) not force the fresh phenotype is treated as the quantitative. –output-missing-phenotype today accepts nonnumeric strings. “–serving checklist” today work securely that have several batches. –oxford-single-chr flag put into allow it to be packing from single-chromosome .gen files that have ignorable SNP ID field viewpoints. –genome don’t fails to statement specific parent-offspring dating. –update-alleles was still shed a few fits connected with missing genotypes; it has been fixed.

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