VNTRview displays genotypying data produced by the VNTRseek program (Paper, Code). Functionality of the VNTRview tabs is described below.
- Home
- The home tab lists the available data samples. Each sample uses a genome identifier plus a suffix that indicates the read length of the original data (example: rl150 indicates read length of 150 bp). Samples can be filtered with a search function which matches characters anywhere in a sample name.
- Stats
- The stats tab lists the meta data about a sample VNTRseek run, including parameters, directories, files, number of reads, number of VNTRs detected, and computation times. Summary files can also be generated from this tab.
- Cluster
- The cluster tab lists the detected clusters. A cluster is a set of reference and read tandem repeats (TR) that were grouped together because of repeat pattern and flanking sequence similarity. Links on this page go to the reference page where the contents of individual clusters can be examined. The clusters table can be filtered and ordered.
- Reference
- The reference tab lists information about the individual reference TRs that were genotyped in the run, the number and kind of alleles detected, and the number of supporting reads for each allele. Links on this page go to the alignment page where the alignment of the reads to the reference TR can be viewed. The references table can be filtered and ordered.
- Alignment
- The alignment tab produces a pdf image of the alignment of the reads mapped to a reference TR. Reads are ordered so that those displaying non-reference VNTR alleles are shown first and further ordered by descending length of the TR array. The number of reads shown in the alignment can be modified.
- Export
- The export tab has buttons for downloading two vcf files and a gff file. The vcf files contain: 1) all genotyped VNTRs (i.e., all TRs that have the minimum number -- usually two -- of supporting reads for a non-reference allele) or 2) all genotyped TRs (i.e., all TRs that have the minimum number of supporting reads for at least one allele, which may or may not be a reference allele). The gff file contains all genotyped VNTRs.