Hi, I used the GATK SplitNCigarReads tools to process RNA-Seq data, which is said to reduce the false positive rate. Then, the processed data was used for SNP calling(by using variant calling tools in GATK). However, after annotating the SNP calling result with GTF file. It shows that only 20%~30% SNP sites locate in the exonic region. I was wonder about it. Ideally, most of the SNP sites may locate in the exonic region. Could u please help me solve this puzzle?
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