Different dbSNP files input yield different variants?
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3 months ago
whb ▴ 20

Hi I was trying to compare if using different dbSNP file as input of BaseRecalibrator and Mutect2 gives different results. and it gave entire different variant list. One gave 16 (REL1505) the other gave 13 (NCBI) variants and there are only 8 common variants.

REL1505: mgp.v5.merged.snps_all.dbSNP142.vcf.gz file in ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/

NCBI: GCA_000001635.6_current_ids.vcf.gz file in ftp://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_2/by_assembly/GCA_000001635.6/

SNP gatk dbSNP mutect2 • 152 views
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