Has anyone ever done variant calling of mitochondrial DNA? There is a bit of information in the supplementary material to the 1000G phase 1 paper, but it's quite limited. Can anyone point me to good resources on this topic? Thanks.
Depends on what you are primarily looking to do, for the clinical panel we used rCRS as the reference sequence and aligned MT reads - there weren't autosomal chromosomes sequenced to begin with but I would suggest you look into Varscan along with GATK (unless thats the only tool supported by your pipeline?!) keeping heteroplasmy in mind.
This might also be a neat read and has some good references http://bioinformatics.oxfordjournals.org/content/29/9/1210.long
Thanks so much for this. I am looking to generate a reference panel and a SNP array among other things. I can use whatever program I want. VarScan seems like a good choice for this to supplement GATK, since it handles extreme coverages well. I'll report back in a few months on my findings. Thanks again.
just wondering which way you ended up going with this analysis? I've been playing with GATK but struggling to have it take into account both the extreme ploidy and coverage...Have not used VarScan before but thinking of trying it out for this. Has it been performing well in your hands for this purpose?
You may also find it useful to check out the pipeline tool MToolBox, specifically designed for variant calling of mtDNA. I am currently using it now for a mtDNA variant study.
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I asked a similar question on the GATK forum just now: http://gatkforums.broadinstitute.org/discussion/1214/can-i-use-gatk-on-non-diploid-organisms