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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.

Tagged:

Issue · Github
by Sheila

Issue Number
1204
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
chandrans

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @johnma
    Hi,

    It sounds like you want to run on the reporter vector alone, which will not work.

    How many samples do you have, and are they whole genome or whole exome?

    I don't think you need to use the flag if you run BaseRecalibrator on enough data. The best thing to do is simply add the reporter as an extra contig to your reference. The tool will be able to detect trends based on the other sites where dbSNP does contain variation. The small reporter regions should not be affected.

    -Sheila

  • johnmajohnma Member

    The thing is I have already finished calling with the reference genome anyway, so I don't feel like doing the whole calling again.

    As for the data, it's a RNA-seq set with 5 samples.

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