版本1.8.0的变化- - - - - - - - - - - - - - - - - - - - - - - - o添加新特性callGenotypes函数注释一组符合二倍体基因型质量,可能等的方式符合gVCF规范。使用的方法有点类似GATK UnifiedGenotyper。版本1.6.0变化- - - - - - - - - - - - - - - - - - - - - - - -新特性添加pileupVariants函数代替阿tallyVariants计算使用Rsamtools核苷酸限速制度,而不是gmapR。在未来,这将使VariantTools gmapR成为独立,但完整的变体统计只会通过tallyVariants可用。用户可见的变化啊,看到这个消息gmapR了解tallyVariants输出的变化。版本1.4.0变化- - - - - - - - - - - - - - - - - - - - - - - -新特性o tallyVariants现在将保持ref行如果variant_strand = 0;这是用于获取信息时没有alt(例如,野生型调用)。最好有一个大集群在整个基因组。添加一个阿keep_extra_stats TallyVariantsParam参数;设置为FALSE将加快速度时,不需要额外的数据。o idVerify现在支持GATK VCF输入,输出。 o callableFraction() now supports GRangesList and TranscriptDb. USER-VISIBLE CHANGES o The API is now based on VRanges, a formal GRanges-derived class for representing variants; use of so-called "tally" or "variant" GRanges is deprecated. o Disable proximity filter by default; we recommend this now only for whole genome calling. o QA filtering is no longer a formal part of the calling pipeline; we recommend to apply QA filters "softly" via qaVariants() and use the results for diagnostics only. o Use BiocParallel (BPPARAM argument) for tallyVariants o VariantTallyParam deprecated; use TallyVariantsParam BUG FIXES o idVerify now correctly computes cliques instead of connected components o use the total count, rather than the ref count when calculating the alt frequency CHANGES IN VERSION 1.2.0 ----------------------- NEW FEATURES o Tally, call and export indels (using same algorithm as for SNVs). o Add post-filter that discards variants that are clumped together on the chromosome (likely mapping errors). o Add filter for masking regions like simple / low complexity repeats. o Add a filter that performs a t-test on the alt vs. ref read positions. o Add callWidtype() function for determining whether a position is variant, wildtype or uncallable, assuming the built-in variant calling filters. This is based on a power calculation that considers the coverage. o Some functions for estimating concordance between samples have been added; these were developed for sample ID verification and should be considered experimental. o matchVariants() utility for matching variants by pos and alt. USER-VISIBLE CHANGES o The VCF output is now always in expanded form (one alt per row). The AD (allele depth) geno tag contains the REF and ALT counts, while AP (allele present) indicates presence of the REF and/or ALT allele. Besides the DP tag, all other tags were removed. These changes bring VariantTools more in line with GATK. o Control alt and total counts are returned from callSampleSpecificVariants. BUG FIXES o The power cutoff in the sample-specific algorithm was not considering the minimum alt read count filter. CHANGES IN VERSION 1.0.0 ----------------------- Initial release (start date: 12 September, 2012)