diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml index e2084dafc0e..2dc3d50e560 100644 --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -85,9 +85,9 @@ Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM d **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. +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. -.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml +.. _Pileup: http://samtools.sourceforge.net/pileup.shtml **Six column pileup**:: @@ -111,7 +111,7 @@ where:: **Ten column pileup** -The `ten-column`__ pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: +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 @@ -137,7 +137,7 @@ where:: 10 Quality values (phred33 scale, see Galaxy wiki for more) -.. __: http://samtools.sourceforge.net/cns0.shtml +.. _consensus: http://samtools.sourceforge.net/cns0.shtml