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Annotation, DNA vs RNA

hjkim123hjkim123 USMember
edited August 2019 in Ask the GATK team

We have WES and RNA data analyzed through GATK pipeline.
All steps were smoothly processed but I noticed a difference between the two after annotation.
The WES data has about 7.7 million variants but 1.5 million variants (19%) are annotated to rsIDs.
The RNA data has around 5.2 million variants but 2.1 million variants (40%) are annotated to rsIDs.
Total number of variants for WES is greater, which is acceptable but the number of annotated rsIDs is half of that of RNA.
The same reference data, dbsnp_138.hg19.vcf, was used.
The variants do not need to be annotated to rsIDs but I am just wondering what possible reasons are for the difference. Any thoughts are welcome.

Thank you for any help.
Post edited by hjkim123 on


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