from BAM datasetsamtools
sam_pileup.py
--input1=$input1
--output=$output1
--ref=$refOrHistory.reference
#if $refOrHistory.reference == "history":
--ownFile=$refOrHistory.ownFile
#else:
--ownFile="None"
#end if
--dbkey=${input1.metadata.dbkey}
--indexDir=${GALAXY_DATA_INDEX_DIR}
--bamIndex=${input1.metadata.bam_index}
--lastCol=$lastCol
--indels=$indels
--mapCap=$mapCap
--consensus=$c.consensus
#if $c.consensus == "yes":
--theta=$c.theta
--hapNum=$c.hapNum
--fraction=$c.fraction
--phredProb=$c.phredProb
#else:
--theta="None"
--hapNum="None"
--fraction="None"
--phredProb="None"
#end if
**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.
.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
------
**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.
.. _Pileup: http://samtools.sourceforge.net/pileup.shtml
**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)
.. _consensus: http://samtools.sourceforge.net/cns0.shtml