mtdna / haplochecker Goto Github PK

Hi, I'm running haplochecker as part of the new Broad GATK Mitochondrial analysis pipeline that uses it in order to estimate contamination.

However, when running it on regular whole genome sequencing data, it is giving illogical contamination estimates:

SampleID Contamination MinorHG MinorLevel MinorSNPs MinorHGvariants MajorHG MajorLevel MajorSNPs MajorHGvariants VerifyScore meanCovVar HG_Distance
UDP-1003_genome.realigned.bam None U8b1b2 0.988 24/30 3 U8b1b2 0.000 24/30 1 0.0 3260.0 0

It is showing the MinorHG as being at a level of 0.988 an the Major HG at a level of 0.0. Also, it is showing the Major and Minor HG as being the same. Must be a few bugs in haplochecker...