What's the merit of running FixMateInformation

[yjx1217]

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!

[glyamamoto]

Hello all,
I was wondering the same.
In the pipeline from GATK (http://gatkforums.broadinstitute.org...ssing-pipeline)

It is said that:
"Indel Realignment
is a two step process. First we create targets using the Realigner Target Creator (either for knowns only, or including data indels), then we realign the targets using the Indel Realigner (see [Local realignment around indels]) with an optional smith waterman realignment. The Indel Realigner also fixes mate pair information for reads that get realigned." (bold is my doing...)

I assume that this "new" version of the Indel Realigner already fixes the mate pairs.
Anyone knows if the assumption is correct and since when?
Many thanks.
Guilherme.

[Jorge Amigo]

there's this discussion that almost addresses this issue: "The indel realigner fixes mates itself, so the file is valid after realignment". but in the same discussion they mention that "The Indel Realigner only fixes the mates of reads that it moves. If your mates information didn't start out correct for other reads, then they will still be wrong even after running through the IR", so I guess that FixMateInformation could still be needed right after the alignment&pairing process to make sure that your bam file is properly handling mate pair information.