What it does
Uses SAMTools' pileup command to produce a pileup dataset from a provided BAM dataset. It generates two types of pileup datasets depending on the specified options. If Call consensus according to MAQ model? option is set to No, the tool produces simple pileup. If the option is set to Yes, a ten column pileup dataset with consensus is generated. Both types of datasets are briefly summarized below.
Types of pileup datasets
The description of pileup format below is largely based on information that can be found on SAMTools Pileup documentation page. The 6- and 10-column variants are described below.
Six column pileup:
1 2 3 4 5 6 --------------------------------- chrM 412 A 2 ., II chrM 413 G 4 ..t, IIIH chrM 414 C 4 ...a III2 chrM 415 C 4 TTTt III7
where:
Column Definition
------- ----------------------------
1 Chromosome
2 Position (1-based)
3 Reference base at that position
4 Coverage (# reads aligning over that position)
5 Bases within reads where (see Galaxy wiki for more info)
6 Quality values (phred33 scale, see Galaxy wiki for more)
Ten column pileup
The ten-column (consensus) pileup incorporates additional consensus information generated with -c option of samtools pileup command:
1 2 3 4 5 6 7 8 9 10 ------------------------------------------------ chrM 412 A A 75 0 25 2 ., II chrM 413 G G 72 0 25 4 ..t, IIIH chrM 414 C C 75 0 25 4 ...a III2 chrM 415 C T 75 75 25 4 TTTt III7
where:
Column Definition
------- --------------------------------------------------------
1 Chromosome
2 Position (1-based)
3 Reference base at that position
4 Consensus bases
5 Consensus quality
6 SNP quality
7 Maximum mapping quality
8 Coverage (# reads aligning over that position)
9 Bases within reads where (see Galaxy wiki for more info)
10 Quality values (phred33 scale, see Galaxy wiki for more)