Pileup

Pileup is a term used in bioinformatics to describe the alignment of multiple sequences of DNA, RNA, or protein to a reference sequence. This alignment is used to identify variations in the sequences, such as single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and structural variants (SVs).

Overview

In bioinformatics, a pileup format is a text-based format for representing a genomic sequence alignment. It is commonly used in genome sequencing projects and genetic variation studies. The format was originally developed for use with the SAMtools software package, but has since been adopted by other bioinformatics tools.

A pileup file contains one line for each position in the reference sequence. Each line includes the reference base, the number of aligned reads covering the position, and the bases and qualities of the aligned reads. This information can be used to identify variations in the sequences.

Variations

Variations identified in a pileup file can include SNPs, indels, and SVs.

• SNPs are variations in a single nucleotide that occurs at a specific position in the genome. They are the most common type of genetic variation among people.
• Indels are insertions or deletions of bases in the genome. They can cause diseases if they disrupt the coding sequence of a gene.
• SVs are large-scale variations in the structure of the genome, such as duplications, inversions, and translocations. They can have a significant impact on gene function and disease.

Tools

Several bioinformatics tools can generate and analyze pileup files, including:

• SAMtools: A suite of programs for interacting with high-throughput sequencing data. It can generate pileup files from BAM or CRAM files.
• BCFtools: A set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. It can analyze pileup files to identify variations.
• VarScan: A platform-independent software tool that can detect variants in NGS data. It can analyze pileup files to identify SNPs, indels, and copy number variations (CNVs).

See also

• Sequence alignment
• Genome sequencing
• Genetic variation

Pileup Resources
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