Documentation

SAMPileupCodec

Decoder for SAM pileup data.

Category ROD Codecs


Overview

From the SAMTools project documentation:

The Pileup format was first used by Tony Cox and Zemin Ning at the Sanger Institute. It describes the base-pair information at each chromosomal position. This format facilitates SNP/indel calling and brief alignment viewing by eye. Note that the pileup program has been replaced in Samtools by mpileup, which produces a slightly different output format by default.

Format

There are two versions of the original pileup format: the current 6-column format produced by Samtools, and the old 10/13-column "consensus" format which could be obtained by using the -c argument, now deprecated.

Simple pileup: 6-column format

Each line consists of chromosome, 1-based coordinate, reference base, the number of reads covering the site, read bases and base qualities. At the read base column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, `ACGTN' for a mismatch on the forward strand and `acgtn' for a mismatch on the reverse strand. A pattern `\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this reference position and the next reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence.

     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<<:<<
 

See the Pileup format documentation for more details.

Consensus pileup: 10/13-column format

The "consensus" or extended pileup consists of the following:

  • original 6 columns as described above
  • 4 extra columns representing consensus values (consensus base, consensus quality, variant quality and maximum mapping quality of the reads covering the sites) for all sites, inserted before the bases and quality strings
  • 3 extra columns indicating counts of reads supporting indels (just for indel sites)

Example of consensus pileup for SNP or non-variant sites

     seq1  60  T  T  66  0  99  13  ...........^~.^~.   9<<55<;<<<<<<
     seq1  61  G  G  72  0  99  15  .............^~.^y. (;975&;<<<<<<<<
     seq1  62  T  T  72  0  99  15  .$..............    <;;,55;<<<<<<<<
     seq1  63  G  G  72  0  99  15  .$.............^~.  4;2;<7:+<<<<<<<
     seq1  64  G  G  69  0  99  14  ..............  9+5<;;;<<<<<<<
     seq1  65  A  A  69  0  99  14  .$............. <5-2<;;<<<<<<;
     seq1  66  C  C  66  0  99  13  .............   &*<;;<<<<<<8<
     seq1  67  C  C  69  0  99  14  .............^~.    ,75<.4<<<<<-<<
     seq1  68  C  C  69  0  99  14  ..............  576<;7<<<<<8<< *
 

Example of consensus pileup for indels

     Escherichia_coli_K12	3995037	*	*\/*	430	0	37	144	*	+A	143	1	0
     Escherichia_coli_K12	3995279	*	*\/*	202	0	36	68	*	+A	67	1	0
     Escherichia_coli_K12	3995281	*	*\/*	239	0	36	67	*	-CG	66	1	0
 

See Consensus pileup format (deprecated) for more details.

Caveat

Handling of indels is questionable at the moment. Proceed with care.


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA