removing dbsnp for indel vcf
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8.1 years ago
morovatunc ▴ 550

Dear all,

Sorry for my ignorance, even though the name of dbsnp implies that its for SNP, I found this part in dbsnp article, Should I apply dbsnp removal to my indel vcf too?

My data is from ICGC consortium. I have one snv and one indel vcfs for every single patient.

Best,

Tunc.

"..database submissions can include a broad range of molecular polymorphisms: single base nucleotide substitutions, short deletion and insertion polymorphisms, microsatellite markers, and polymorphic insertion elements such as retrotransposons."

vcf • 2.0k views
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hi, dbSNP does contain InDels as well. A primer here. So you might want to filter dbSNP InDels. Though the relevance or lack of it depends on your biological question.

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For some reason, dbsnp annotation of indel vcf is taking too long. I wanted to be sure that if I need to do this.

Thank you very much for your answer

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