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,
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
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!
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