Oxford-format transfer today tolerates identical A1/A2 allele rules

  • 5 August 2022
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Oxford-format transfer today tolerates identical A1/A2 allele rules

twenty six February: “–recode vcf” heading changed getting compatibility having VCFtoolspact one thousand Genomes stage 1 data files printed to the tips web page.

Single-reliability digital matrix efficiency (age

dos March: –bcf today handles BCFv2.dos nonzero destroyed genotype and you may prevent-of-vector beliefs (released from the e.g. bcftools step one.1) properly. –mendel-multigen no longer is prohibited because of the demand-line parser when a family-built association test is work on. –shed, –freq, –hardy, and –het now service gzipped yields (range from the ‘gz’ modifier). –R added to invention make.

15 January: –keep/–eliminate today works properly to the newly-current IDs whenever –update-ids is in the exact same manage. –mac/–max-mac placed into innovation create.

12 January: –dose + –covar + –sex today works securely, and you may an inaccurate caution about the PLINK step one.07 execution might have been removed. –dose logistic regression no more records improper p-viewpoints for very small examples.

(beta 3): –epistasis implemented, with heavy optimization for quantitative traits. “–recode vcf” 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-labels, –neighbor, –mh/–bd/–mh2/–homog and –clump-field bugfixes. –q-score-range then followed for dosage data. –split-x/–merge-x ‘no-fail’ modifier put in service analysis sales scripts.

Digital –length efficiency bugfix

13 December: Case/handle –hardy/–hwe no longer randomly excludes a lot of regulation off manage-merely phase away from sample. (This is generally simple, once the all the-products shot still did, and insect was only going to exist whenever –hardy/–hwe was at an equivalent work at once the most other filter systems such as –exclude/–pull. But if you used the UNAFF rows regarding –hardy report to have anything, you should rerun –sturdy on current create. ) set-decide to try numerous-investigations modification today counts nonempty establishes having no high versions.

7 December: –to alter today relates to the new joint attempt statistic rather than the ingredient feeling in the event the previous try calculated, without offered account linearly genomic-controlled p-beliefs when they will be incorrect. Certain numeric balances advancements to possess brief p-viewpoints. –logistic permutation make sure –assoc/–model put-shot bugfixes. –linear/–logistic put-ensure that you –amount ‘sex’ modifier followed. –dosage + –gender mistake message today teaches you you to definitely PLINK step one.07 failed to deal with it flag integration properly.

twenty five November: Fixed –exclude/–pull memory management bug in 2 November build. –get today aids dose data. –write-serving no further produces incorrect IDs whenever test strain try applied. –serving ‘noheader’ is now able to be taken having ‘list’ whenever for every single batch has only you to file. –assoc/–model lay-attempt then followed. –set-missing-var-ids expanded to permit addition of allele brands, and you will –set-missing-snp-ids/–set-missing-nonsnp-ids resigned. UNADJ line philosophy are in reality correct from inside the “–to switch gc” profile.

dos November: Enhanced variant ID browse speed. grams. –make-grm-bin) has become considering double-reliability interior calculations, therefore the ‘bin’ + ‘single-prec’ modifier consolidation has been substituted for ‘bin4’.

fifteen Oct: Repaired a bug within the –vcf’s management of variants with ten or more alternate alleles. –serving Zout no longer segfaults in the bottom. Merger not scrambles centimorgan coordinates.

20 Sep: Repaired non-strict –biallelic-merely bug whenever dealing with multiallelic variants. When you yourself have used –biallelic-merely versus ‘strict’ into VCF data having triallelic versions, i strongly recommend rerunning new procedure towards newest build. Repaired decimal feature –assoc insect one brought about it to enter for each and every output https://datingranking.net/es/citas-crossdresser/ line double, and you will –linear/–logistic mishandling of some datasets which have heterozygous haploid phone calls. –vcf-min-gp put into development create.

18 September: –no-fid bugfix. Exposure off nonnumeric phenotype chain (e.grams. ‘NA’) no more force the fresh phenotype becoming managed as quantitative. –output-missing-phenotype today allows nonnumeric chain. “–amount checklist” today performs properly which have numerous batches. –oxford-single-chr flag added to ensure it is packing away from solitary-chromosome .gen records that have ignorable SNP ID industry values. –genome not does not report specific parent-kids relationships. –update-alleles was still forgotten several matches related to destroyed genotypes; this has been repaired.