twenty-six March: “–recode vcf” header altered to own being compatible having VCFtoolspact one thousand Genomes stage 1 investigation data files printed to your resources web page.
Single-precision binary matrix productivity (age
2 February: –bcf now protects BCFv2.2 nonzero shed genotype and you will stop-of-vector beliefs (emitted of the elizabeth.grams. bcftools 1.1) properly. –mendel-multigen is no longer prohibited by command-line parser when a household-oriented organization try are work with. –forgotten, –freq, –sturdy, and you can –het today help gzipped production (are the ‘gz’ modifier). –Roentgen added to development build.
15 January: –keep/–dump today really works properly towards freshly-upgraded IDs when –update-ids is within the exact same focus on. –mac/–max-mac computer placed into invention create.
twelve January: –serving + –covar + –intercourse now functions safely, and you will an incorrect caution towards PLINK step one.07 execution has been removed. –dose logistic regression no longer profile incorrect p-values for really 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, –neighbour, –mh/–bd/–mh2/–homog and you will –clump-community bugfixes. –q-score-range accompanied to possess amount investigation. –split-x/–merge-x ‘no-fail’ modifier put into service study sales scripts.
Digital –length efficiency bugfix
13 December: Case/control –hardy/–hwe not any longer at random excludes way too many control away from manage-only stage regarding sample. (This was primarily innocuous, due to the fact all of the-products sample nonetheless did, and bug was just browsing are present when –hardy/–hwe was a student in an identical focus on given that other strain including –exclude/–extract. But if you utilized the UNAFF rows on the –sturdy statement getting something, you ought to rerun –hardy with the most recent create. ) set-decide to try numerous-comparison modification today counts nonempty set having no high alternatives.
7 December: –adjust today relates to new combined take to figure instead of the ingredient effect in the event the previous is calculated, and no longer records linearly genomic-managed p-thinking after they was invalid. Specific numeric balances advancements getting short p-values. –logistic permutation ensure that you –assoc/–model set-decide to try bugfixes. –linear/–logistic lay-make sure –serving ‘sex’ modifier observed. –dose + –gender error message now teaches you you to definitely PLINK step 1.07 failed to handle so it flag consolidation safely.
25 November: Repaired –exclude/–extract memory administration bug in 2 November create. –score today aids dose investigation. –write-dosage don’t writes incorrect IDs whenever shot strain try used. –serving ‘noheader’ are now able to be used that have ‘list’ when per batch only has one to document. –assoc/–model place-take to observed. –set-missing-var-ids prolonged to permit inclusion out of allele brands, and you can –set-missing-snp-ids/–set-missing-nonsnp-ids retired. UNADJ column values are actually right from inside the “–to improve gc” accounts.
2 November: Enhanced variation ID lookup price. grams. –make-grm-bin) has grown to become according to twice-accuracy internal data, in addition to ‘bin’ + ‘single-prec’ modifier combination could have been replaced with ‘bin4’.
fifteen Oct: Repaired an insect inside –vcf’s management of variations which have 10 or even more choice alleles. –dosage Zout no longer segfaults in the bottom. Merger no further scrambles centimorgan coordinates.
20 September: Repaired non-rigid –biallelic-only insect whenever addressing multiallelic variants. If you have put –biallelic-just rather than ‘strict’ on VCF data that have triallelic variations, i highly recommend rerunning the brand new procedure into the latest build. Fixed quantitative feature –assoc bug you to definitely caused it to enter for every productivity range twice, and –linear/–logistic mishandling of a few datasets which have heterozygous haploid calls. –vcf-min-gp put into development make.
18 Sep: –no-fid bugfix. Presence out-of nonnumeric phenotype strings (elizabeth.grams. ‘NA’) no more force the new phenotype to-be addressed because decimal. –output-missing-phenotype today accepts nonnumeric strings. “–serving number” now really works safely having several batches. –oxford-single-chr banner set in make it loading away from single-chromosome https://datingranking.net/es/citas-crossdresser/ .gen data files with ignorable SNP ID profession beliefs. –genome no longer fails to statement specific moms and dad-young ones relationships. –update-alleles had been shed several fits connected with destroyed genotypes; this has been repaired.