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about dbsnp files

BogdanBogdan Palo Alto, CAMember ✭✭

Dear Geraldine, and all,

as the BUNDLES contains 2 vcf files that are associated with dbSNP, particularly for hg19 :

1) dbsnp_138.hg19.excluding_sites_after_129.vcf
2) dbsnp_138.hg19.vcf

which file 1) or 2) would you recommend to use for BSQR or or variant score recalibration ?

much thanks,

bogdan

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