Dear all, I' really new to the use of Galaxy, NGS analysis and SNP calling. I have a problem. After that I generate pileup and filter some reads with the SAMtools filter pileup The resulting data set contain about 2200 SNPs At least I compare my result data set whit dbSNP132.txt and 1kg.lc.2010_7.CEU.liftedhg19.pgSnp. The resulting data set contain 700 SNPs. Now the question: The problem is that I must have 200 SNPs instead of 700.... I have check the resutls and I saw that some result are duplicated for all parameters but had a different rs ID. how can I remove the wrong one??? please help me. some one I heard about SOAPsnp but I don't know how to use. Could anyone please help me. Thanks Francesco --