My data is RNAseq with single end reads. I used the Bowtie to generate the Bam file. And I want to call SNP using Samtools. I want to find the sites under RNA editing (from C-T or G-A). I hypothesize them as the SNP sites. I view the bam file by IGV, and lots of regions have these SNP variations. So I use the samtools and bcftools to call SNP. But it only produce very few sites as SNP.
Why samtools can not find all SNP sites by my data? Anyone can give me some suggestions?