BMD 427 Applied Bioinformatics Lecture 6: Variant Calling Analysis

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What does variant calling entail?

Identifying single nucleotide polymorphisms (SNPs) and small deletions

What is the reference for germline variant calling?

The standard for the species of interest

Which of the following is NOT a type of genomic variant mentioned in the text?

Large deletions

What is the advantage of variant calling?

In-depth analysis of all aspects of genetic variation including SNPs, InDel, SV, SNV

What does somatic variant calling refer to?

Reference tissue from the same individual

How many approaches to identifying structural variants are mentioned in the text?

4

What is the process by which we identify variants from sequence data?

Variant calling

Which method involves mapping the sequencing reads to a reference genome and identifying variants based on the differences between the reads and the reference genome?

Alignment-based methods

Which file format offers better lossless compression than BAM and full compatibility with BAM?

CRAM file

What does RNA-seq primarily focus on?

Allele-specific expression

Which tool is used for variant calling and involves de novo assembly-based methods?

ABySS

What is the major challenge in variant calling due to alignment errors?

Ambiguous alignment at the end of the read

What is the characteristic readalignment pattern for variant calling in NGS?

Differences highlighted in red in the reads

'Posterior probability' is used to quantify statistical evidence in which aspect of variant calling?

Determining posterior probability cutoff

'CRAM' file format is primarily associated with which process?

Compressed alignments

'Hybrid methods' in variant calling combine which two types of approaches?

De novo assembly-based and alignment-based

Test your understanding of Variant Calling: Single-Nucleotide Variants, Indels, and Structural Variants in this quiz based on the lecture by Marwa Amer, PhD. Explore the identification approaches for structural variants and key insights from Alkan et al. (2011).

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