Matthew, Galaxy's pileup samtools wrapper does not use -v at all. Setting the 'Whether or not to print only output pileup lines containing indels' option to 'Print only lines containing indels' sets -i. Thanks, Kelly On Wed Jul 13, at 6:53 PM, Matthew McCormack wrote:

Is choosing 'Print only lines containing indels' in the 'Whether or not to print only output lines containing indels' drop down for Generate pileup, the same as the -v option in SAMTools pileup ?

Matthew

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