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Genotyping for dbSNPS

senguptadsenguptad SingaporeMember

In a project I need see the allelic frequency for dbSNPs in the RNAseq data of a single cell. To be precise, given the dbsnp I need 0/0s as well if there is required coverage of reads. SNV calling pipeline normally does not report if it is 0/0. I have come all the way to recalibrated BAM following the RNAseq SNV calling best practice as suggested in GATK site. Help with the command would be highly appreciated.

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