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BQSR without dbsnp as the --known database

kezkez CardiffMember

Hi GATK,

I have run the BQSR but I only included two databases for the -known parameter;
1000G_phase1.indels
Mills_and_1000g_gold_standard_indels

I realise I should have included the dbsnp_138 database in this list. Is it necessary to re-run with all three databases? How much difference will it make to the variant calling analysis?

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