Hi there,
I saw a few NGS data processing piplelines have a "fix mate information" step by either running picard tools or samtools after finished the GATK local realignment. But in the newest GATK workflow(http://www.broadinstitute.org/gsa/wi..._indel_calling), there is not such a step. So I want to ask what's the merit of running the "fix mate information" step after local realignment and is this step still necessary? Thanks!
I saw a few NGS data processing piplelines have a "fix mate information" step by either running picard tools or samtools after finished the GATK local realignment. But in the newest GATK workflow(http://www.broadinstitute.org/gsa/wi..._indel_calling), there is not such a step. So I want to ask what's the merit of running the "fix mate information" step after local realignment and is this step still necessary? Thanks!
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