Mitochondrial LiftoverVcf
I run Mito pipeline follow :
However, the LiftoverVcf step is really confusing.
In GATK pipeline, it recommends using`AddOATag (picard)` in LiftoverVcf step.
The output of `AddOATag` is a bam file that can't be used for MergeVcfs.
What is the right way to do LiftoverVcf ?
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Hi Fiona Liang
Looks like there is a confusion between document pages and the original Mitochondria short variant discovery page. The page directed from the main document goes to a 4.1.4.0 version of the LiftoverVcf page which seems to be the confusing part. If you look at the page for 4.4.0.0 version of the same tool it reflects the actual tool and its usage
https://gatk.broadinstitute.org/hc/en-us/articles/13832753098907-LiftoverVcf-Picard-
I hope this helps.
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Thank you so much!
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