Hello, I have sequenced whole genome mitochondrial samples. I calculated the fold 80 base penalty using CollectHsMetrics(GATK). But I am getting above 100, which I think is incorrect. The code which I used for calculating is the below code
gatk CollectHsMetrics -I /mnt/NGS2/MitoRes/Batch_20/10255168_26/BAM_Files/10255168_26_MtMkDupSorted.bam \ -O /mnt/NGS2/MitoRes/Batch_20/10255168_26/BAM_Files/10255168_26_MtMkDupSorted_metrics.txt \ -R /mnt/NGS2/Database/Homo_sapiens_assembly38.chrM.fasta \ -BI /mnt/NGS2/Database/Twist_MitoPanel_chrM_all_hg38_target.interval_list \ -TI /mnt/NGS2/Database/Twist_MitoPanel_chrM_all_hg38_target.interval_list
For this particular sample, I am getting Fold-80 as 40. So then I used the parameter
-covMax 2000 and the score went down to 4.
So I wanted to know the correct value for
-covMax while calculating fold 80 for mitochondrial Data. And what is the optimum result we should get for mitochondrial data?