Pileup format explained

Pileup
Extensions:.msf, .pup, .pileup
Developer:Tony Cox and Zemin Ning
Type:Bioinformatics
Extended From:Tab separated values

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 byTony Cox and Zemin Ning at the Wellcome Trust Sanger Institute, and became widely known through its implementation within the SAMtools software suite.[1]

Format

Example

Sequence Position Reference Base Read Count Read Results Quality
seq1 272 T 24,.$.....,,.,.,...,,,.,..^+.
seq1 273 T 23 ,.....,,.,.,...,,,.,..A
seq1 274 T 23 ,.$....,,.,.,...,,,.,...
seq1 275 A23 ,$....,,.,.,...,,,.,...^l.
seq1 276 G 22 ...T,,.,.,...,,,.,....
seq1 277 T 22 ....,,.,.,.C.,,,.,..G.
seq1 278 G 23 ....,,.,.,...,,,.,....^k.
seq1 279 C 23 A..T,,.,.,...,,,.,.....

The columns

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

Column 6: The base quality string

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

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

External links

Notes and References

  1. 10.1093/bioinformatics/btp352 . 2009 . Bioinformatics . 25 . 2078–2079 . 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 . 1000 Genome Project Data Processing Subgroup (2009). 16 . 19505943 . 2723002 .
  2. Web site: QUANTA: Protein Design. 3. Reading and Writing Sequence Data Files . . 1998-10-02 . . 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 . 10.1186/1471-2105-12-31 . 1471-2105 . 3037855 . 21261974 . free .
  4. Web site: Chisom . Halimat . 2023-03-31 . File Formats Every Bioinformatician — Established or Upcoming — Must Know (and then some) . 2023-11-11 . Medium . en.