MitoHPC_Process

Run MitoHPC_process script for summary files

Filters applied

Variant level filters applied

-- FILTER column: no "strict_strand|strand_bias|base_qual|map_qual|weak_evidence|slippage|position|Homopolymer|clustered|fragment|haplotype"
-- INFO column: no "INDEL|HP(homopolymer region)", no Read_depth < 300
-- no biallelic het variants (for each sample only one het at each POS)

Sample level filters generated (all samples are kept in the per_sample file, with different filter flags)

-- suspicious contamination from MitoHPC
-- Copy number <= 40
-- het_count > 5

README file for summary outputs

README_MitoHPC_summary.txt

Twist pre_process

Pre process fastq files and map to reference to generate BAM files for MitoHPC

-- Run twist_pipeline.sh script interactively to generate BAM files

01/27/2026

- Update mito_genome_annotation file with the latest UKB dropout count and rate

12/05/2025

- Add README file that explains the columns within each summary file

10/09/2025

- Add heteroplasmy filter for the two false positive variants (12705_C_T and 12684_G_A)

05/14/2025

- Add twist_preprocess scripts for processing fastq files

05/08/2025

- Add mito_genome_reference file for all annotation
- Update process script for the new reference file

06/26/2024

- Update script for mMSS calculation; add new_mito_score_m file

02/21/2024

- Add script for MitoHPC output processing; add new_mito_score file