SNP calling from RNAseq data

YogeshYogesh south koreaMember

Hi,
Do I need to do Indel Realignment and Base Recalibration while calling SNP from RNAseq data?
If yes, then please share the command line.
What are the parameter that should be used for raw VCF filtering?

Please also share any documents/text related to SNP calling from RNAseq as well as DNAseq with command lines.

Thanks
Yogesh

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