filtering by mapping quality

igorigor New YorkMember

I've been following GATK Best Practices for WGS/WES. It's very comprehensive. One thing that's missing is any mention of mapping quality filtering. A lot of tools are already using MappingQualityFilter internally by default, so it's already implemented in a way. Why not just filter out reads with low mapping quality right after alignment? Would that affect the results (maybe indels)?

Answers

  • EADGEADG KielMember

    Hi igor,

    if you want to filter out reads by mapping quality, you can use samtools view with the option -q .

    But be aware UG, HTC and mutect are handeling mapQ in different ways e.g. have different default values for their mapQ-Filters.

    Greetings EADG

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @igor
    Hi,

    We usually don't like to remove any original data.

    In the past, IndelRealigner would assign a higher mapping quality to reads that had shifted after the reassembly. So, some reads that may have had low original mapping quality could have higher mapping quality after Indel Realignment.

    Also, I think HaplotypeCaller also assigns a higher mapping quality to reads that are shifted during the reassembly. So, it is best to have all the reads in the region even if the mapper did not do a perfect job at aligning them.

    -Sheila

  • igorigor New YorkMember

    @Sheila said:
    In the past, IndelRealigner would assign a higher mapping quality to reads that had shifted after the reassembly. So, some reads that may have had low original mapping quality could have higher mapping quality after Indel Realignment.

    Also, I think HaplotypeCaller also assigns a higher mapping quality to reads that are shifted during the reassembly. So, it is best to have all the reads in the region even if the mapper did not do a perfect job at aligning them.

    I understand mapping qualities can get readjusted, but how much can they change? I don't think they can go up more than 10. Or can they?

    For example, I assume if I filter reads below MQ 10, those reads would still be below MQ 20 even after additional adjustments, so they are low quality regardless.

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