Query related to SNP calling from RNAseq data using GATK

I have few queries related to SNP detection in RNAseq data:

1) Is it required to do Indel Realignment and Base Recalibration while calling SNP from RNAseq data?

2) When I used RNAseq data for SNP calling, I also got SNP in intron region also.why?

snp

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written 9.3 years ago by Bioinfonext

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