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VCF from RNA-seq data

AmmuAmmu Member
edited March 13 in Ask the GATK team
I would like to determine variants from RNA-seq data that was generated in different lanes. I've combined it during alignment step using HISAT2 and the uniquely mapped reads to the ref. genome is 80%. Can I use this bam file from the step 2 (ie. Add read groups, sort, mark duplicates, and create index) onwards in GATK Best Practices workflow for SNP and indel calling on RNAseq data?

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