Hi Dario, Thank you for help last time. I wonder if deepSNV and shearwater were designed to call variants from exome-seq (genome wide) data or it is designed just for calling variants from small scale data (like few genes...) When i try to run deepSNV for single exon i got an error library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene tx_Exons<-exonsBy(txdb) gr<-tx_Exons[1:3] dpSNV1<-deepSNV(test="test.sorted.bam",control="control.sorted.bam",re gions=gr[1],combine.method="fisher") Error: class(regions) %in% c("data.frame", "GRanges") is not TRUE Thank you very much. [[alternative HTML version deleted]]

Hello, The error message is clear. You need to provide a GRanges or data.frame variable for the regions of interest. If you read about exonsBy by opening the help page using ?exonsBy, you will see the returned variable is a GRangesList. Changing it to regions = gr[[1]] would test each exon of the first transcript in the GRangesList. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia