Structural Variant (SV) calling with SVdetect 2019
Overview
Most approaches for predicting structural variants require you to have paired-end or mate-pair reads. They use the distribution of distances separating these reads to find outliers and also look at pairs with incorrect orientations. As mentioned during several of the presentations, many researchers choose to ignore these types of mutations and combined with the increased difficulty of accurately identifying them, the community is less settled on the "best" way to analyze them. Here we present a tutorial on SVDetect based on the quality of its instructions, and easy of installation despite its use of relatively hefty configuration files.
Other possible tools:
- BreakDancer - hard to install prerequisites on TACC. Requires installing libgd and the notoriously difficult GD Perl module.
- PEMer - hard to install prerequisites on TACC. Requires "ROOT" package.
Good discussion of some of the issues of predicting structural variation:
Example: E. coli genome with structural variation
Here's an E. coli genome re-sequencing sample where a key mutation producing a new structural variant was responsible for a new phenotype involving citrate, something the Barrick lab has studied.
cds cp -r $BI/gva_course/structural_variation/data GVA_sv_tutorial cd GVA_sv_tutorial
This is Illumina mate-paired data (having a larger insert size than paired-end data) from genome re-sequencing of an E. coli clone.
File Name | Description | Sample |
---|---|---|
| Paired-end Illumina, First of mate-pair, FASTQ format | Re-sequenced E. coli genome |
| Paired-end Illumina, Second of mate-pair, FASTQ format | Re-sequenced E. coli genome |
| Reference Genome in FASTA format | E. coli B strain REL606 |
NC_012967.1.lengths | Simple tab delimtered file based on the size of the reference needed for SVDetect so you don't have to create it yourself |
Map data using bowtie2
First we need to (surprise!) map the data. This will hopefully reinforce the bowtie2 tutorial you just completed, but if you are feeling adventurous you could use BWA as optional reinforcement.
Do not run on head node
Make sure you are on an idev node using the command: showq -u
Welcome to the University Wiki Service! Please use your IID (yourEID@eid.utexas.edu) when prompted for your email address during login or click here to enter your EID. If you are experiencing any issues loading content on pages, please try these steps to clear your browser cache. If you require further assistance, please email wikihelp@utexas.edu.