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Variant Calling and Visualization DNASeq Lab II
Meg Staton edited this page Sep 28, 2016
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- To understand different types of variants that can be detected with NGS
- To explore variant calling software - usual workflow, difficulties, statistics, file formats
- To practice calling variants with samtools
- Slides
- Lab - DNA Seq II - Variant Calling and IGV Visualization
- What are SNPs, SNVs, Indels
- What are the analysis steps to go from raw DNA reads to variants? What software packages are available for each step of analysis?
- What are some of the difficulties/sources of errors in identifying variants?
- Many variant callers employe Bayesian methods. What types of information are included in the models?
- What is a genotype likelihood score?
- What types of filtering are often used for variant calls and why?
- What is imputation? Can you do imputation without a reference genome? Why or why not?
- What type of information does a vcf file store? How is it different/similar to the bcf file format?
- Samtools and bcftools - what file formats do they manipulate and what are some common things they do?
HW5 Due Monday, October 3rd