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As I know GATK is worked fine for Genome SNP Calling. Can I know it work well for Transcriptome SNP calling as well? I can't find much info regarding Transcriptome SNP calling.
If yes, can I know the step for Transcriptome SNP calling by GATK is same as what we did for Genome SNP calling? eg. alignment raw read to reference transcriptome, marking/remove PCR duplicates, local realignment around indel and quality score re-calibration (if know dbSNP is available).
Thanks and looking forward to hear from you.