The Variation Analysis Service can be used to identify and annotate sequence variations. The service enables users to upload one or multiple short read samples and compare them to a closely related reference genome. For each sample, the service computes the variations against the reference and presents a detailed list of SNPs, MNPs, insertions and deletions with confidence scores and effects such as “synonymous mutation” and “frameshift.” High confidence variations are downloadable in the standard VCF format augmented by SNP annotation. A summary table illustrating how the variations are shared across the samples is also available.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
The code in this module provides the BV-BRC application service wrapper scripts for the Variation Analysis Service as well as some backend utilities:
| Script name | Purpose |
|---|---|
| App-Variation.pl | App script for the Variation Analysis Service |
| var-map.pl | Script for aligning reads and identifying sequence variations |
| var-annotate.pl | Script for the annotation of the sequence variations |
| var-combine.pl | Script for combining the variation analysis results of all samples |
Li, H. (2014) Towards better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics, btu356.
Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods, 9, 357-359.
Lee, W.P., Stromberg, M.P., Ward, A., Stewart, C., Garrison, E.P. and Marth, G.T. (2014) MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One, 9, e90581.
Frith, M.C., Hamada, M. and Horton, P. (2010) Parameters for accurate genome alignment. BMC bioinformatics, 11, 1.
Marth, G.T., Korf, I., Yandell, M.D., Yeh, R.T., Gu, Z., Zakeri, H., Stitziel, N.O., Hillier, L., Kwok, P.-Y. and Gish, W.R. (1999) A general approach to single-nucleotide polymorphism discovery. Nature genetics, 23, 452-456.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. and Genome Project Data Processing, S. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
Cingolani, P., Platts, A., Wang, L.L., Coon, M., Nguyen, T., Wang, L., Land, S.J., Lu, X. and Ruden, D.M. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6, 80-92.
Li H. (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100.