SNP Detection
The SNP detection feature in Avadis NGS identifies the variants (SNPs/MNPs/InDels) in a sample by comparing the aligned reads against the reference genome. Based on the distribution of As, Ts, Gs, and Cs at a particular position, and the likelihood of a sequencing error, a judgement is made with regards to the existence of a SNP.
The SNP detection algorithm in Avadis NGS works on a per-sample basis. For each sample, data for each chromosome is analyzed, with a capability for parallel computation per chromosome. The computation is optimized for memory usage by segregating the data into windows based on maximum read size.
Below we illustrate how the following three key SNP analysis steps can be performed in Avadis NGS:
- Display and enumerate the SNPs/InDels
- Display confidence in the SNP/InDel call
- Bin the SNPs/InDels based on a consequence filter
Display and enumerate the SNPs/InDels
The SNP detection feature can be invoked on exome, whole genome and transcriptome samples. The first two types of samples can be loaded into Avadis NGS as a DNA-Seq experiment. Transcriptome samples are loaded into Avadis NGS as an RNA-Seq experiment. Once the experiment is created, the Sequence Analysis section of the Workflow pane on the right contains a step called SNP Detection.
Clicking on this workflow step will enable the user to detect SNPs in a chosen read list. The chosen read list could be the list of all reads that were imported into the experiment, or any other filtered read list. In addition, the following parameters can be set for the SNP detection algorithm:
Once the SNP detection step finishes, a SNP results object is created in the navigator. Double-clicking on the SNP result object launches the inspector for the results. The inspector includes the SNPs, MNPs, INs and DELs discovered for each sample.
In addition, a folder called SNP Region Lists is created, that contains one SNP results region list for each sample. Double-clicking on this SNP region list object launches the inspector that displays and enumerates all the SNPs/InDels.
It is also possible to visualize these SNPs/InDels in a couple of intuitive ways:
Dragging and dropping either the SNP results object, or the individual sample SNP result region lists into the genome browser will show all the SNPs and InDels in the genome browser. One can navigate over the SNPs in the genome browser very easily using the navigator buttons. The track can be filtered as well as colored according to a variety of properties.
The other visualization is called the "Variant Support View" and can be invoked from right-clicking on the SNP results object. This view is especially useful for verifying heterozygous SNPs in a more convenient way than the genome browser.
Display confidence in the SNP/InDel call
When SNP detection is invoked it allows setting a cut-off on the confidence measure (also called decibel score) of the SNPs.
The decibel score for each SNP can be viewed in the SNP region list inspector as show below.
The decibel score for each SNP can also be viewed in the genome browser as shown below.
Bin the SNPs/InDels based on a consequence filter
The biological consequences of SNPs can be identified by running the SNP Effect Analysis workflow step. It is necessary to choose the desired transcript annotations to execute this step. For example, for human hg18 samples, one can choose to use Ensembl, RefSeq, or UCSC transcript annotations as shown below.
The effects determined by this step fall into the following categories:
The resulting region list of a SNP Effect Analysis can again be inspected as shown below.
Or it can be dragged and dropped into the genome browser, as shown below.
Additional Information
If you have any question on this or any other features of Avadis NGS, our software support is available around-the-clock by phone and avadisngs [dot] support [at] strandsi [dot] com (email). Training and services can also be provided for diverse research requirements.
