Hi, dear list. We are right now using Galaxy for the pileup of some of our BAM files, but we also would like to be able to use samtools to generating the same results on our own PC. The options we use on the web interface are the simplest, as shown in this screenshot: http://imgur.com/WCwVBvG Can anyone inform us what are the commands and options under the hood? Thanks! Best regards, Kaiyin ZHONG ------------------------------ Forensic Molecular Biology, Erasmus MC k.zhong@erasmusmc.nl kindlychung@gmail.com