Variant Analysis - Accurate Sequence Variant Calling

Sequence variant analysis in RTG Investigator provides accurate Indel and SNP calling for variant detection and variant calling in cancer genome and human genome project research.  This integrated variant analysis pipeline can deliver a 290-fold improvement in variant calling accuracy when applied in a consensus filter approach.  Click here for a description of optimized variant analysis.   Click here for a detailed introduction to the core pipeline and its capability for accurate variant detection.

SNP calling - RTG identifies 192,250 additional SNPs for analysis.

Variant call sets for NA12878 were compared between RTG map / RTG snp and BWA / GATK pipelines.

Bayesian SNP, MNP and INDEL Caller An innovative design integrates a probabilistic aligner for local realignment of read data around complex regions and assesses genome sequence ambiguity in a single processing operation. The variant caller produces posterior scores that help identify the vast majority of true variants in whole genome sequencing or exome data (for benchmark studies, see our variant detection white paper).
Multi-platform SNP Combining reads from different sequence technologies delivers higher variant call accuracy. The RTG snp command can apply platform-specific base quality information from both Illumina and Complete Genomics sequencing platforms to adjust variant call scoring. In a test with NA19240 reads, plotting true positive vs false positive variant calls at progressively higher posterior scores shows variant calls with the combined CG + Illumina read data to be more accurate than with either CG or Illumina data alone.
Coverage Observing and comparing read depths across genomic loci supports experimental quality assurance. The RTG coverage command measures coverage depth at each base pair and reports in industry standard BED format.  Sensitivity tuning parameters allow an investigator to identify the most appropriate set of alignments for downstream analysis.
Copy Number Variation Comparing two genomes against a reference across loci shows large scale duplications and deletions, particularly useful in cancer genomics. The RTG cnv command calculates the ratio of coverage at each loci between a test genome and a base genome. Bucket size can be adjusted for data smoothing. Filter settings allow different analytical comparisons with the same alignments.