[galaxy-user] SamTools Filter Pileup "Only report variants?" option is misleading

In using the filter pileup tool we've discovered that the option "Only report variants?" will throw away lines that have indels provided that they do not contain any SNPs. For example the line: chr1 88427041 C 38 ..+1A..+1A.....+1A.,..+1A.....,.+1A,.,......,...,^~.^~,^~,^~, HHHHHFEHHHHHBFHHHHHHBFHHHEHHHAHHHFHG#E will not be included in the filtered results. At the very least we would recommend relabeling the option to "Only report SNP variants?" But it would also be helpful to include an option to filter for both SNP and indel variants. Thanks! -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123