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Call Varients from RNA-seq for RNA editing detection
Dear GATK staff
I would like to use the GATK tool for the detection of possible RNA editing events. I followed the RNA-seq best practice up to the variant calling step itself. There I hesitate to use the haplotype caller because I would not assume that the editing sites follow any kind of allelic ratio. Therefore I wanted to ask if it might be better to use MuTec2 at this stage? I would call it like ...
java -jar GenomeAnalysisTK.jar -T MuTect2 -R reference.fasta -I:tumor normal1.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0 --dbsnp dbSNP.vcf --artifact_detection_mode -o output.normal1.vcf java -jar GenomeAnalysisTK.jar -T CombineVariants -R reference.fasta -V output.normal1.vcf -V output.normal2.vcf -minN 2 --setKey "null" --filteredAreUncalled --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED -o MuTect2_PON.vcf
Can you comment if this is a suitable modification of the best practice in the case of RNA editing calls?