Hi Matthew, The output will have the datatype assigned as 'tabular'. Assign this as 'mpileup' to have the filter tool recognize the dataset. Another option is to use 'MPileup' with default options (" Genotype Likelihood Computation: as positive" creates a .bcf output). To change tabular -> mpileup, click on the pencil icon in the upper top right corner of the dataset, then in the middle pane choose the tab 'Datatype', pick "mpileup' from the menu, and save. Best, Jen On 4/22/14 10:53 AM, Matthew wrote:

I used Bowtie2 on a fastq file. Then, generate pileup on the output of Bowtie2. When I try to use 'Filter pileup', there is no file recognized as input even though I have the output from the 'Generate pileup'.

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