# 安装htslib$ conda install htslib# 压缩vcf文件$ bgzip-c vcf.file>vcf.file.gz# 对压缩文件进行索引$ tabix-p vcf vcf.file.gz 所有文件准备好之后就可以使用vcfeval命令进行比较了: $ rtg vcfeval-b~/raw_vcf/ref/HG002_hg19_GIAB_highconf.ccds.vcf.gz-c~/raw_vcf/HG002_SNP.vcf.gz-o output...
RTG vcfeval在单倍型水平上执行变异比较,也就是说,它确定在比较的 VCF 中声明的基因型在应用于参考基因组时是否会产生相同的基因组序列。 这本身就是一个不平凡的问题,而幼稚的方法面临着组合爆炸,以确定最准确的分析。 迄今为止,没有其他工具能够像 RTG vcfeval那样准确、快速地执行这种分析。 RTG 于 2010 年开...
BSD Licensed source code ongithub Over the years one of the more valuable tools we've developed for internal testing and development purposes is an accurate and efficient way to compare genotypes from multiple VCFs for a set of individuals. In particular, our tool, vcfeval, is capable of deal...
BSD Licensed source code ongithub Over the years one of the more valuable tools we've developed for internal testing and development purposes is an accurate and efficient way to compare genotypes from multiple VCFs for a set of individuals. In particular, our tool, vcfeval, is capable of deal...
Have you checked the docs? nf-core website: troubleshooting nf-core modules documentation Description of the bug To use the vcfeval engine in hap.py executable of RTG(tools) is needed within the container. RTG seems to be absent in curre...
RTGvcfevalperforms variant comparison at the haplotype level, that is, it determines whether the genotypes asserted in the VCFs under comparison result in the same genomic sequence when applied to the reference genome. This in itself is a non-trivial problem and naive approaches face a combinatoria...