details: http://www.bx.psu.edu/hg/galaxy/rev/3e194c33f219 changeset: 2760:3e194c33f219 user: Anton Nekrutenko <anton@bx.psu.edu> date: Thu Sep 24 11:55:55 2009 -0400 description: small help and parameter name tweaks 2 file(s) affected in this change: tools/samtools/sam_pileup.xml tools/samtools/sam_to_bam.xml diffs (103 lines): diff -r cbb7103283fe -r 3e194c33f219 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Wed Sep 23 19:11:12 2009 -0400 +++ b/tools/samtools/sam_pileup.xml Thu Sep 24 11:55:55 2009 -0400 @@ -56,13 +56,13 @@ </param> <param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" /> <conditional name="c"> - <param name="consensus" type="select" label="Whether or not to call the consensus sequence using the MAQ consensus model"> - <option value="no">Don't use MAQ consensus model</option> - <option value="yes">Use the MAQ consensus model</option> + <param name="consensus" type="select" label="Call consensus according to MAQ model?"> + <option selected="true" value="no">No</option> + <option value="yes">Yes</option> </param> <when value="no" /> <when value="yes"> - <param name="theta" type="float" value="0.85" label="Theta paramter (error dependency coefficient) in the MAQ consensus calling model" /> + <param name="theta" type="float" value="0.85" label="Theta parameter (error dependency coefficient) in the MAQ consensus calling model" /> <param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" /> <param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" /> <param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" /> @@ -77,9 +77,68 @@ **What it does** -Uses SAMTools_' pileup command to produce a file in the pileup format based on the provided BAM file. +Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM dataset. It generated two types of pileup datasets depending on chosen 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_ documentation page. The 6- and 10-column variants are described below. + +.. _SAMTools: 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`__ pileup incoroporates 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) + + +.. __: http://samtools.sourceforge.net/cns0.shtml + </help> </tool> diff -r cbb7103283fe -r 3e194c33f219 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml Wed Sep 23 19:11:12 2009 -0400 +++ b/tools/samtools/sam_to_bam.xml Thu Sep 24 11:55:55 2009 -0400 @@ -51,7 +51,7 @@ **What it does** -This tool uses the SAMTools_ toolkit to produce a BAM file based on a sorted input SAM file. +This tool uses the SAMTools_ toolkit to produce a indexed BAM file based on a sorted input SAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml