2.5 years ago by
That particular tool uses pileup as a datatype input, not VCF.
To obtain a pileup dataset, use the Mpileup or Generate pileup without the option genotype liklihood calculation. At the end of the run, the output will be in tabular format. Use the pencil icon to change the type to pileup and use the data with downstream tools, such as Filter Pileup.
To work with VCF datasets, see the tool group NGS: VCF Manipulation.
Details about all of these options are on the tool forms, both in the top option setting area and below in the help.
Thanks, Jen, Galaxy team