Does GATK variant discovery make use of unpaired alignments and discordant alignments?

I've searched for this and cannot find the answer. Suppose a BAM file contains Illumina paired-end reads with the following types of alignments:

1) Properly paired alignments (both mates mapped with the proper orientation and within the expected distance)
2) Discordant pairs (both mates are mapped, but not properly paired)
3) Unpaired alignments (singletons, only one of the mates is mapped)

Does the GATK variant discovery process make use of the discordant pairs and unpaired alignments? If so, what would be the consequence of excluding the discordant pairs and singletons?


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I think HaplotypeCaller uses all properly mapped reads in analysis. Perhaps this thread will help too.

    In good quality "clean" regions, the assumption is that there won't be many discordant pairs or unpaired alignments, so discounting those should not make much difference.


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