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!
Masonic Cancer Center
University of Minnesota