BMD 427 Applied Bioinformatics Lecture 6: Variant Calling Analysis

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 Signup and view all the answers

What does somatic variant calling refer to?

Reference tissue from the same individual Signup and view all the answers

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

4 Signup and view all the answers

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

Variant calling Signup and view all the answers

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 Signup and view all the answers

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

CRAM file Signup and view all the answers

What does RNA-seq primarily focus on?

Allele-specific expression Signup and view all the answers

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

ABySS Signup and view all the answers

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

Ambiguous alignment at the end of the read Signup and view all the answers

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

Differences highlighted in red in the reads Signup and view all the answers

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

Determining posterior probability cutoff Signup and view all the answers

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

Compressed alignments Signup and view all the answers

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

De novo assembly-based and alignment-based Signup and view all the answers