mitochondria-pipeline

Based on mitochondria m2 wdl

Steps

1. SubsetBamToChrM
2. RevertSam
3. AlignAndCall
4. --- AlignToMt/AlignToShiftedMT AlignAndMarkDuplicates
   ------- picard samtofastq
   ------- bwa-mem
   ------- picard mark duplicates
   ------- picard sort sam
5. --- scatter: CollectWgsMetrics
6. --- scatter: Call M2
7. --- scater?: LiftoverAndCombineVcfs
8. --- MergeStats
9. --- InitialFilter
10. --- SplitMultiAllelicsAndRemoveNonPassSites
11. --- GetContamination
12. --- FilterContamination
13. --- FilterNuMTs
14. --- FilterLowHetSites
15. ConvergeAtEveryBase
16. SplitMultiAllelicSites

Dashboard ⋅ BUILD: Mitochondria Pipeline

https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0/chrM?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false