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[edit | edit source]
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[edit | edit source]
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[edit | edit source]
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[edit | edit source]
| Pileup Resources | |
|---|---|
|
 |
Search WikiMD
Ad.Tired of being Overweight? Try W8MD's physician weight loss program.
Semaglutide (Ozempic / Wegovy and Tirzepatide (Mounjaro / Zepbound) available.
Advertise on WikiMD
|
WikiMD's Wellness Encyclopedia |
| Let Food Be Thy Medicine Medicine Thy Food - Hippocrates |
Translate this page: - East Asian
中文,
日本,
한국어,
South Asian
हिन्दी,
தமிழ்,
తెలుగు,
Urdu,
ಕನ್ನಡ,
Southeast Asian
Indonesian,
Vietnamese,
Thai,
မြန်မာဘာသာ,
বাংলা
European
español,
Deutsch,
français,
Greek,
português do Brasil,
polski,
română,
русский,
Nederlands,
norsk,
svenska,
suomi,
Italian
Middle Eastern & African
عربى,
Turkish,
Persian,
Hebrew,
Afrikaans,
isiZulu,
Kiswahili,
Other
Bulgarian,
Hungarian,
Czech,
Swedish,
മലയാളം,
मराठी,
ਪੰਜਾਬੀ,
ગુજરાતી,
Portuguese,
Ukrainian
Medical Disclaimer: WikiMD is not a substitute for professional medical advice. The information on WikiMD is provided as an information resource only, may be incorrect, outdated or misleading, and is not to be used or relied on for any diagnostic or treatment purposes. Please consult your health care provider before making any healthcare decisions or for guidance about a specific medical condition. WikiMD expressly disclaims responsibility, and shall have no liability, for any damages, loss, injury, or liability whatsoever suffered as a result of your reliance on the information contained in this site. By visiting this site you agree to the foregoing terms and conditions, which may from time to time be changed or supplemented by WikiMD. If you do not agree to the foregoing terms and conditions, you should not enter or use this site. See full disclaimer.
Credits:Most images are courtesy of Wikimedia commons, and templates Wikipedia, licensed under CC BY SA or similar.
Contributors: Prab R. Tumpati, MD
