Variant Annotation Tool

[…] was sequenced in more than 80% of accessions. sites with indels, more than two alleles, or more than 10% missing data were further excluded. snps were classified as synonymous or non-synonymous by variant annotation tool v.2.0.1 (ref. ). relicts were identified with the same method as before: the median distance of each accession to all others was calculated, and relicts were defined […]

[…] other vcf annotation tools are snpeff [] and snpsift []. snpeff can perform annotation for multiple variants and snpsift allows rapid detection of significant variants from the vcf files []. the variant annotation tool (vat) distinguishes itself from other annotation tools in one aspect by adding cloud computing capabilities []. vat annotation occurs at the transcript level to determine […]

[…] in total, combining data obtained with the two approaches, we identified 25,516 novel single-nucleotide polymorphisms (snps) and 9144 novel indels (fig.  and s1). we annotated our vcf files using variant annotation tool version 2.0.1 (habegger et al. ). for this analysis we focused on lof variants, considering the importance of their likely biological consequences as well as their increased […]

[…] relaxation of purifying selection, and/or an increased mutation rate , ., p-values were computed for significance of enrichment by gorilla (http://cbl-gorilla.cs.technion.ac.il/)., using the variant annotation tool (version 2.0.1.) with the gencode v7 annotation , we examined snps and indels for variants predicted to result in the complete loss-of-function (lof). lof variants […]