I have searched for RNA-Seq variant calling programs and got a list of several programs. Could anyone suggest which program should be most reliable for cancer transcriptome data? (I meant RNA-Seq variant calling program without genome/exome data) Here is the list of programs I found.
SNVMix2
RNASEQR
SNVQ
SNV-pipeline-v1.0
SAMtools mpileup -> bcftools
VarScan
SNVMix2
RNASEQR
SNVQ
SNV-pipeline-v1.0
SAMtools mpileup -> bcftools
VarScan
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