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ReassignMappingQuality and variant calling

gatk2013gatk2013 Member
edited June 2013 in Ask the GATK team


I'm trying to call variants from bowtie-aligned reads, I used PrintReads with ReassignMappingQuality filter to give all reads a mapping score of 60 to replace default value of 255. However, I'm wondering if this assignment would introduce any bias in variant calling.

Thanks a lot!

Best Answers


  • Thank you, Carneiro. Bowtie doesn't report mapping qual (255 for not available). Actually I'm just testing if it is okay to use bowtie with gatk.

  • @Geraldine_VdAuwera said:
    We do have users who report using data aligned with Bowtie, and assigning qualities using the ReassignMappingQuality filter, but we recommend using an aligner that does report mapping qualities. Having a reasonably accurate estimate of mapping quality empowers the GATK tools to distinguish real variants from artifacts.

    Thanks a lot. I got it.

  • bowtie2 reports an 'alignment score' in the optional AS:i and XS:i fields of a SAM file. bowtie2 has some advantages over bwa. instead of pushing bwa maybe gatk ought to consider the AS:i field if it's available.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @virenpatel, it is not practical for us to start taking into account alternative metrics that are stored in optional fields. Presumably if this alignment score was directly equivalent to mapping quality, that's where it would be reported. Since it's reported elsewhere, chances are it is calculated differently and has a different meaning. If so we would need to build in additional utilities in order to convert the values appropriately into mapping qualities. If this was trivial I assume the developers of bowtie would have their tool generate the mapping qualities directly. So I'm sorry, but no, we can't do that.

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