DRAGEN_Analysis

BED files

1. CMRG_5030.bed - This file contains all 5,030 challenging medically relevant gene (CMRG) regions
2. FixItFelix.collapsed.sorted.bed - This contains the regions that are impacted due to collapsed errors in the GRCh38 reference
3. FixItFelix.duplicated.sorted.bed - This contains the regions that are impacted due to duplicated errors in the GRCh38 reference
4. FixItFelix_12_CMRG.sorted.bed - This file contains the CMRG regions that are impacted due to either collapsed or duplicated errors

Counting basepairs

1. count_basepair.py - This script counts the total impacted basepairs of all variants at the sample level. It can be run with Tuvari-4.1-dev (https://github.com/ACEnglish/truvari)
2. count_bp_SNV_INDEL_chr21.json - Sample output file of the script
3. dragen_sv_merge.py - script for merging STR, SV and VCF files at sample level (check the dragen_sv_merge_notes file for additional information)

STR benchmarking

1. truvari_giabtr_testing.pdf - This document contains the detailed description of STR benchmarking analysis
2. Truvarizer.py - script used in the STR analysis
3. EHVCFConverter.py - script used to convert DRAGEN STR vcf to truvari recognizable format