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Threshold for base phred quality

faithmifaithmi United StatesMember
edited October 2014 in Ask the GATK team

Hi, when I looked at the call_stats output from MuTect, I am wondering does MuTect only count the reads with base phred quality > 5 in the t_ref_count, t_alt_count, n_ref_count, n_alt_count fields? (I got this conclusion by looking at the base phred quality of each read in IGV). If so, is there any way to change the threshold for the base phred quality? Thanks!



  • vyellapavyellapa Member

    I have similar question on base quality thresholds used by Mutect. Is there a threshold used at all? If so, would the time consuming BQSR help at all.

    Thank you,

  • faithmifaithmi United StatesMember

    Hi Teja,

    I figured out that there are thresholds in MuTect, the threshold for the base phred quality is 5. There are descriptions for all thresholds and filters in the supplemental material of MuTect paper.

    I don't think threshold directly related to whether you should do BQSR or not....For me, I think BQSR is always a necessary step to go through.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @vyellapa‌ What @faithmi explains is correct. Regarding BQSR, it is useful because the base qualities are taken into account when MuTect weighs the amount of evidence for each allele.

  • epinatelepinatel ItalyMember

    Dear Geraldine,
    I have maybe a trivial question but as Mutect has filters based on base phred quality, which phred qualities it expects? You can use it also on IlluminaGAIIX output directly (Phred 64) or you need to convert them to Phred+33 ?
    Thank you in advance

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