Hi Jesse, We agree that the original "pileup" tool does not have all of the functionality that one might want. The tool authors seem to also agree, and developed an upgraded version called "mpileup". This has recently been wrapped and added to the Galaxy main public instance in the same 'NGS: SAM Tools' tool group. The 'MPileup SNP and indel caller' tool form has a summary of the available options and links to the full documentation, including the SAMTools' authors and support/discussion groups. Thanks for the feedback and hopefully you will find the Mpileup tool useful and/or SAMTools discussion groups a helpful resource, Best, Jen Galaxy team On 1/26/12 8:38 AM, Jesse Erdmann wrote:

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!

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support