plink and mitochondrial DNA

Question

[Ram]

Hello everyone,

I'm using a pipeline developed by another bioinformatician in the team a couple of years ago - someone who is no longer in the team. This pipeline uses plink - module loads it without specifying a version number.

The pipeline also has an awk script that maps X,Y and MT chromosomes to 23,24 and 25 respectively. The current plink standard is to map MT to 26, because 25 maps to the Pseudo Autosomal Region of X and Y.

Was there a time when MT mapped to 25 for plink - I'm trying to understand why the bioinformatician mapped MT to 25.

Answer 1

[chrchang523]

I don't think so. The original plink changelog at http://pngu.mgh.harvard.edu/~purcell/plink/changelog.shtml mentions that XY and MT were added together in mid-2007.

[Ram]

Thank you! Turns out, the pipeline wasn't built to handle MT CNVs - this is the first time we're seeing one, so I'm gonna have to update the pipeline.