What is the fold 80 base penalty of Mitochondrial Data?
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9 weeks ago
NikhilP ▴ 20

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?

Thank you.

NGS mitochondiral • 176 views

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