Jump to content

Pileup format: Difference between revisions

Add links
From Wikipedia, the free encyclopedia
Browse history interactively
← Previous edit
Content deleted Content added
VisualWikitext
Adding local short description: "File format for sequence data", overriding Wikidata description "file format used in the field of Bioinformatics"
 
(27 intermediate revisions by 19 users not shown)
Line 1: Line 1:
{{Short description|File format for sequence data}}
{{Infobox file format
| name = Pileup
| extensions = .msf, .pup, .pileup
| developer = Tony Cox and Zemin Ning
| type = [[Bioinformatics]]
| extended_from = [[Tab separated values]]
| url = {{URL|http://www.htslib.org/doc/samtools-mpileup.html}}
}}

'''Pileup format''' is a text-based [[File format|format]] for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of [[Single-nucleotide polymorphism|SNP]]/indel calling and alignment. It was first used by
'''Pileup format''' is a text-based [[File format|format]] for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of [[Single-nucleotide polymorphism|SNP]]/indel calling and alignment. It was first used by
Tony Cox and Zemin Ning at the [[Wellcome Trust Sanger Institute]], but became widely known through its implementation within the [[SAMtools]] software suite.
Tony Cox and Zemin Ning at the [[Wellcome Trust Sanger Institute]], and became widely known through its implementation within the [[SAMtools]] software suite.
<ref name="Li et al 2009">
<ref name="Li et al 2009">{{cite journal
|doi=10.1093/bioinformatics/btp352 |date=2009 |journal = Bioinformatics |volume=25 |pages=2078–2079 |title=The Sequence alignment/map (SAM) format and SAMtools
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) ''The Sequence alignment/map (SAM) format and SAMtools''. '''Bioinformatics''', 25:2078-9. [http://www.ncbi.nlm.nih.gov/pubmed/19505943 PubMed]
|author1=Li H. |author2= Handsaker B. |author3= Wysoker A. |author4= Fennell T. |author5= Ruan J.
</ref>
|author6= Homer N. |author7=Marth G. |author8= Abecasis G. |author9= Durbin R | author10= 1000 Genome Project Data Processing Subgroup (2009)|issue=16 |pmid=19505943 |pmc=2723002 }}</ref>


==Format==
==Format==


===Example===
===Example===
{| class="wikitable"
⚫
<pre>seq1 272 T 24 ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&
|-
⚫
seq1 273 T 23 ,.....,,.,.,...,,,.,..A <<<;<<<<<<<<<3<=<<<;<<+
! Sequence !! Position !! Reference Base !! Read Count !! Read Results !! Quality
⚫
seq1 274 T 23 ,.$....,,.,.,...,,,.,... 7<7;<;<<<<<<<<<=<;<;<<6
|- style="font-family: monospace;"
⚫
seq1 275 A 23 ,$....,,.,.,...,,,.,...^l. <+;9*<<<<<<<<<=<<:;<<<<
seq1 276 G 22 ...T,,.,.,...,,,.,.... 33;+<<7=7<<7<&<<1;<<6<
| seq1 || 272 || T || 24|| ,.$.....,,.,.,...,,,.,..^+. || {{code|2=bf|1=<<<+;<<<<<<<<<<<=<;<;7<&}}
|- style="font-family: monospace;"
⚫
seq1 277 T 22 ....,,.,.,.C.,,,.,..G. +7<;<<<<<<<&<=<<:;<<&<
seq1 278 G 23 ....,,.,.,...,,,.,....^k. %38*<<;<7<<7<=<<<;<<<<<
| seq1 || 273 || T || 23 || ,.....,,.,.,...,,,.,..A || {{code|2=bf|1=<<<;<<<<<<<<<3<=<<<;<<+}}
|- style="font-family: monospace;"
⚫
seq1 279 C 23 A..T,,.,.,...,,,.,..... ;75&<<<<<<<<<=<<<9<<:<<<
⚫
| seq1 || 274 || T || 23 || ,.$....,,.,.,...,,,.,... || {{code|2=bf|1=7<7;<;<<<<<<<<<=<;<;<<6}}
</pre>
|- style="font-family: monospace;"
⚫
| seq1 || 275 || A|| 23 || ,$....,,.,.,...,,,.,...^l. || {{code|2=bf|1=<+;9*<<<<<<<<<=<<:;<<<<}}
|- style="font-family: monospace;"
⚫
| seq1 || 276 || G || 22 || ...T,,.,.,...,,,.,.... || {{code|2=bf|1=33;+<<7=7<<7<&<<1;<<6<}}
|- style="font-family: monospace;"
⚫
| seq1 || 277 || T || 22 || ....,,.,.,.C.,,,.,..G. || {{code|2=bf|1=+7<;<<<<<<<&<=<<:;<<&<}}
|- style="font-family: monospace;"
⚫
| seq1 || 278 || G || 23 || ....,,.,.,...,,,.,....^k. || {{code|2=bf|1=%38*<<;<7<<7<=<<<;<<<<<}}
|- style="font-family: monospace;"
⚫
| seq1 || 279 || C || 23 || A..T,,.,.,...,,,.,..... || {{code|2=bf|1=75&<<<<<<<<<=<<<9<<:<<<}}
|}


===The columns===
===The columns===
Line 25: Line 47:
#Number of aligned reads covering that position (depth of coverage)
#Number of aligned reads covering that position (depth of coverage)
#Bases at that position from aligned reads
#Bases at that position from aligned reads
#quality of those bases (OPTIONAL)
#Phred Quality of those bases, represented in ASCII with -33 offset (OPTIONAL)


===Column 5: The bases string===
===Column 5: The bases string===
*. (dot) means a base that matched the reference on the forward strand
*. (dot) means a base that matched the reference on the forward strand
*, (comma) means a base that matched the reference on the reverse strand
*, (comma) means a base that matched the reference on the reverse strand
*</> (less-/greater-than sign) denotes a reference skip. This occurs, for example, if a base in the reference genome is intronic and a read maps to two flanking exons. If quality scores are given in a [[Pileup_format#Column_6:_The_base_quality_string|sixth column]], they refer to the quality of the read and not the specific base.
⚫
*AGTCN denotes a base that did not match the reference on the forward strand
*agtcn denotes a base that did not match the reference on the reverse strand
*AGTCN (upper case) denotes a base that did not match the reference on the forward strand
⚫
*agtcn (lower case) denotes a base that did not match the reference on the reverse strand
⚫
*A sequence matching the [[regular expression]] \+[0-9]+[ACGTNacgtn]+ denotes an insertion of one or more bases starting from the next position
*A sequence matching the regular expression -[0-9]+[ACGTNacgtn]+ denotes a deletion of one or more bases starting from the next position
*A sequence matching the [[regular expression]] {{code|2=ragel|\+[0-9]+[ACGTNacgtn]+}} denotes an insertion of one or more bases starting from the next position. For example, +2AG means insertion of AG in the forward strand
⚫
*A sequence matching the regular expression {{code|2=ragel|\-[0-9]+[ACGTNacgtn]+}} denotes a deletion of one or more bases starting from the next position. For example, -2ct means deletion of CT in the reverse strand
*^ (caret) marks the start of a read segment and the ASCII of the character following `^' minus 33 gives the mapping quality
*^ (caret) marks the start of a read segment and the ASCII of the character following `^' minus 33 gives the mapping quality
*$ (dollar) marks the end of a read segment
*$ (dollar) marks the end of a read segment
* * (asterisk) is a placeholder for a deleted base in a multiple basepair deletion that was mentioned in a previous line by the -[0-9]+[ACGTNacgtn]+ notation
* * (asterisk) is a placeholder for a deleted base in a multiple basepair deletion that was mentioned in a previous line by the {{code|2=ragel|-[0-9]+[ACGTNacgtn]+}} notation
*< (less-than sign) reference skip
*> (greater-than sign) reference skip


===Column 6: The base quality string===
===Column 6: The base quality string===
Line 44: Line 65:


==File extension==
==File extension==
There is no standard [[file extension]] for a Pileup file, but .msf (multiple sequence file), .pup<ref>{{cite web |url=http://www.esi.umontreal.ca/accelrys/life/quanta2K/protein/03_Sequence_data_files.html |title=QUANTA: Protein Design. 3. Reading and Writing Sequence Data Files |author=[[Accelrys]] |date=1998-10-02 |publisher=[[Université de Montréal]] |access-date=2020-03-27}}</ref> and .pileup<ref>{{Cite journal |last1=Glez-Peña |first1=Daniel |last2=Gómez-López |first2=Gonzalo |last3=Reboiro-Jato |first3=Miguel |last4=Fdez-Riverola |first4=Florentino |last5=Pisano |first5=David G |date=2011-01-24 |title=PileLine: a toolbox to handle genome position information in next-generation sequencing studies |journal=BMC Bioinformatics |volume=12 |pages=31 |doi=10.1186/1471-2105-12-31 |issn=1471-2105 |pmc=3037855 |pmid=21261974 |doi-access=free }}</ref><ref>{{Cite web |last=Chisom |first=Halimat |date=2023-03-31 |title=File Formats Every Bioinformatician — Established or Upcoming — Must Know (and then some) |url=https://medium.com/@gearthdexter/bioinformatics-file-formats-3919a26b7679 |access-date=2023-11-11 |website=Medium |language=en}}</ref> are used.
There is no standard [[file extension]] for a Pileup file, but .pileup is commonly used.


==See also==
==See also==
Line 58: Line 79:
*[https://github.com/wwood/bioruby-pileup_iterator bioruby-pileup_iterator (A Ruby pileup parser)]
*[https://github.com/wwood/bioruby-pileup_iterator bioruby-pileup_iterator (A Ruby pileup parser)]
*[http://wwwfgu.anat.ox.ac.uk/~andreas/documentation/samtools/usage.html pysam (A Python pileup parser)]
*[http://wwwfgu.anat.ox.ac.uk/~andreas/documentation/samtools/usage.html pysam (A Python pileup parser)]

{{Bioinformatics}}


[[Category:Bioinformatics]]
[[Category:Bioinformatics]]

Latest revision as of 02:25, 27 December 2023

Pileup
Filename extensions
.msf, .pup, .pileup
Developed byTony Cox and Zemin Ning
Type of formatBioinformatics
Extended fromTab separated values
Websitewww.htslib.org/doc/samtools-mpileup.html

Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP/indel calling and alignment. It was first used by Tony Cox and Zemin Ning at the Wellcome Trust Sanger Institute, and became widely known through its implementation within the SAMtools software suite. [1]

Format

[edit]

Example

[edit]
Sequence Position Reference Base Read Count Read Results Quality
seq1 272 T 24 ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&
seq1 273 T 23 ,.....,,.,.,...,,,.,..A <<<;<<<<<<<<<3<=<<<;<<+
seq1 274 T 23 ,.$....,,.,.,...,,,.,... 7<7;<;<<<<<<<<<=<;<;<<6
seq1 275 A 23 ,$....,,.,.,...,,,.,...^l. <+;9*<<<<<<<<<=<<:;<<<<
seq1 276 G 22 ...T,,.,.,...,,,.,.... 33;+<<7=7<<7<&<<1;<<6<
seq1 277 T 22 ....,,.,.,.C.,,,.,..G. +7<;<<<<<<<&<=<<:;<<&<
seq1 278 G 23 ....,,.,.,...,,,.,....^k. %38*<<;<7<<7<=<<<;<<<<<
seq1 279 C 23 A..T,,.,.,...,,,.,..... 75&<<<<<<<<<=<<<9<<:<<<

The columns

[edit]

Each line consists of 5 (or optionally 6) tab-separated columns:

  1. Sequence identifier
  2. Position in sequence (starting from 1)
  3. Reference nucleotide at that position
  4. Number of aligned reads covering that position (depth of coverage)
  5. Bases at that position from aligned reads
  6. Phred Quality of those bases, represented in ASCII with -33 offset (OPTIONAL)

Column 5: The bases string

[edit]
  • . (dot) means a base that matched the reference on the forward strand
  • , (comma) means a base that matched the reference on the reverse strand
  • </> (less-/greater-than sign) denotes a reference skip. This occurs, for example, if a base in the reference genome is intronic and a read maps to two flanking exons. If quality scores are given in a sixth column, they refer to the quality of the read and not the specific base.
  • AGTCN (upper case) denotes a base that did not match the reference on the forward strand
  • agtcn (lower case) denotes a base that did not match the reference on the reverse strand
  • A sequence matching the regular expression \+[0-9]+[ACGTNacgtn]+ denotes an insertion of one or more bases starting from the next position. For example, +2AG means insertion of AG in the forward strand
  • A sequence matching the regular expression \-[0-9]+[ACGTNacgtn]+ denotes a deletion of one or more bases starting from the next position. For example, -2ct means deletion of CT in the reverse strand
  • ^ (caret) marks the start of a read segment and the ASCII of the character following `^' minus 33 gives the mapping quality
  • $ (dollar) marks the end of a read segment
  • * (asterisk) is a placeholder for a deleted base in a multiple basepair deletion that was mentioned in a previous line by the -[0-9]+[ACGTNacgtn]+ notation

Column 6: The base quality string

[edit]

This is an optional column. If present, the ASCII value of the character minus 33 gives the mapping Phred quality of each of the bases in the previous column 5. This is similar to quality encoding in the FASTQ format.

File extension

[edit]

There is no standard file extension for a Pileup file, but .msf (multiple sequence file), .pup[2] and .pileup[3][4] are used.

See also

[edit]

References

[edit]
  1. ^ Li H.; Handsaker B.; Wysoker A.; Fennell T.; Ruan J.; Homer N.; Marth G.; Abecasis G.; Durbin R; 1000 Genome Project Data Processing Subgroup (2009) (2009). "The Sequence alignment/map (SAM) format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352. PMC 2723002. PMID 19505943.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  2. ^ Accelrys (1998-10-02). "QUANTA: Protein Design. 3. Reading and Writing Sequence Data Files". Université de Montréal. Retrieved 2020-03-27.
  3. ^ Glez-Peña, Daniel; Gómez-López, Gonzalo; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino; Pisano, David G (2011-01-24). "PileLine: a toolbox to handle genome position information in next-generation sequencing studies". BMC Bioinformatics. 12: 31. doi:10.1186/1471-2105-12-31. ISSN 1471-2105. PMC 3037855. PMID 21261974.
  4. ^ Chisom, Halimat (2023-03-31). "File Formats Every Bioinformatician — Established or Upcoming — Must Know (and then some)". Medium. Retrieved 2023-11-11.
[edit]
Retrieved from "https://en.wikipedia.org/enwiki/w/index.php?title=Pileup_format&oldid=1192004233"