├── 1kg_summary ├── README.md ├── annotate.sh ├── convert_anno.py ├── convert_anno.sh ├── count_gt.py ├── count_gt.sh ├── count_var_cohort.py ├── count_var_cohort.sh ├── count_var_sample.py ├── count_var_sample.sh ├── get_allele_freq_novel_func.py ├── get_allele_freq_novel_func.sh ├── hash_msvcf.py ├── hash_msvcf.sh ├── join_gtc_anno.py ├── join_gtc_anno.sh ├── summary1 │ ├── summarize_cohort_var_count.py │ ├── summarize_cohort_var_count_print.py │ ├── summarize_sample_var_count.py │ └── summarize_sample_var_count_print.py └── summary2 │ ├── print_freq_novel.py │ ├── print_freq_novel_func.py │ └── summary_freq_novel_func.py ├── Benchmarking.txt ├── CMRG_389.bed ├── CMRG_5030.bed ├── EHVCFConverter.py ├── FixItFelix.collapsed.sorted.bed ├── FixItFelix.duplicated.sorted.bed ├── FixItFelix_12_CMRG.sorted.bed ├── GangSTRConvertTruvariCompatible.py ├── HG002_SVs_Tier1_v0.6.DEL.1kbp.vcf ├── README.md ├── Truvarizer.py ├── benchmarking └── makefile ├── config_wittyer_CNV.json ├── 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