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",regions=gr[1],combine.method="fisher")

Error: class(regions) %in% c("data.frame", "GRanges") is not TRUE



Thank you very much.

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