Hello everyone!
I would appreciate some advice regarding the filtering of structural variants.
The variant caller used for discovery-“DELLY or DELLY2”using whole-genome sequencing and Whole exome sequencing data across multiple samples.
Murtadha Shukur
Choose a variant caller: Several tools can detect SVs from WGS/WES data. Popular options include Manta, Delly, and Lumpy. Quality score filtering: Set a minimum quality score threshold to retain high-confidence SV calls. Quality scores indicate the variant caller's confidence in the identified variant. Depth filtering: Filter out SVs with low read depth, as these could be artifacts from sequencing errors. Strand bias filtering: Remove SVs with significant strand bias, where reads supporting the variant come predominantly from one strand. Database filtering: Exclude SVs present in public databases of known polymorphisms like dbSNP to focus on potentially novel variants. Functional impact filtering: Annotate the remaining SVs using tools like SIFT or MutationTaster to assess their potential impact on protein function. Sample-specific filtering: Consider incorporating information about the patient's phenotype and family history to prioritize relevant SVs.
Filtering structural variants (SVs) from WGS/WES data is a crucial step in identifying potentially disease-causing mutations. Here's a breakdown of the process:
Challenges with WES data:
- Short-read sequencing used in WES makes SV detection less sensitive compared to WGS due to limitations in capturing large genomic rearrangements.
- Consider using specific SV detection tools designed for WES data for better accuracy.
General Filtering Steps:
Additional Tips:
- Use visualization tools like IGV to inspect SVs in the genomic context.
- Consider variant filtering workflows offered by platforms like GATK or specific analysis pipelines designed for SV analysis.
Remember, this is a general guideline. The specific filtering criteria will depend on your research question and the analysis tools you use.
0 votes
0 thanks
- Badges
- Science topic
- Similar topics
- Filing
More Chandana Veshala's questions See All
Similar questions and discussions