I have recently performed a variant annotation using Snpeff in water buffalo. The variants were called through bcftools call program (multiallelic caller) from Samtools package and are based on RNAseq reads. The BAM files were produced by aligning the RNAseq reads on the water buffalo genome available in NCBI Genome website.
SnpEff annotated many variants as downstream gene variants which is not right because the variants are called based on RNAseq reads. Can anyone throw any light on this?