版本1.8.0的变化-----------------------新功能o添加callGenotypes函数，用于注释一组具有二倍体基因型质量、可能性等的计数，以符合gVCF规范的方式。方法有点类似于GATK UnifiedGenotyper使用的方法。版本1.6.0的变化-----------------------新功能o添加pileupvariables函数，作为tallyvariables的替代品，使用Rsamtools计算核苷酸堆积，而不是gmapR。在未来，这将允许VariantTools独立于gmapR，但是完整的变量统计数据将只能通过tallyvariables获得。用户可见的变化o查看gmapR的新闻，了解tallyvariables输出的变化。版本1.4.0的变化-----------------------新特性o tallyvariables现在将保持ref行如果variant_strand=0;这对于在没有alt时获取信息非常有用(例如，用于进行wildtype调用)。最好有一个大的集群在整个基因组上做这个。o在TallyVariantsParam中添加keep_extra_stats参数;将此设置为FALSE将在不需要额外数据时加快速度。o idVerify现在支持VCF输入，如GATK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)