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BQSR: Is it safe to use run_without_dbsnp_potentially_ruining_quality in this case?
In this particular situation, after calling variants using a genome assembly reference, we would also want to see where there are any variations accumulated in the reporter vector, and as such the reference in this case is the reporter gene sequence (<1.5kb).
I wonder in this case it is safe for me to put on the -run_without_dbsnp_potentially_ruining_quality tag? I haven't noticed any person reporting variants in reporter vectors.