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Contaminaton very high in Mutect mitochondrial pipeline
Hi, I ran the mitochondrial pipeline on a standard Truseq WGS genome sample, but I got contamination 0.98. See here for contamination metrics:
SampleID Contamination MinorHG MinorLevel MinorSNPs MinorHGvariants MajorHG MajorLevel MajorSNPs MajorHGvariants VerifyScore meanCovVar
UDP-1003_genome.realigned.bam None U8b1b2 0.988 24/30 3 U8b1b2 0.000 24/30 1 0.0 3260.0
Not sure how this is possible or what this means. i.e. how is the minor HG 0.98 but the major one 0 ?