diff --git a/data/modules/covsnap/NA12878_panel.covsnap.json b/data/modules/covsnap/NA12878_panel.covsnap.json new file mode 100644 index 00000000..85d41479 --- /dev/null +++ b/data/modules/covsnap/NA12878_panel.covsnap.json @@ -0,0 +1,164 @@ +{ + "covsnap_version": "0.5.0", + "schema_version": "1.0", + "run": { + "sample_name": "NA12878_panel", + "bam_path": "/data/NA12878_panel.bam", + "reference": null, + "engine_used": "mosdepth", + "engine_version": "0.3.8", + "contig_style": "chr", + "run_date": "2026-06-29", + "bed_path": null, + "exon_only": false, + "thresholds": [ + 1, + 5, + 10, + 20, + 30, + 50, + 100 + ], + "classify_params": { + "pass_pct_ge_20": 95.0, + "pass_max_pct_zero": 1.0, + "dropout_pct_zero": 5.0, + "dropout_zero_block_bp": 500, + "uneven_cv": 1.0, + "exon_pct_ge_20": 90.0, + "exon_max_pct_zero": 5.0 + } + }, + "summary": { + "n_targets": 2, + "n_pass": 2, + "status_counts": { + "PASS": 2 + } + }, + "targets": [ + { + "target_id": "BRCA1", + "contig": "chr17", + "start": 43044294, + "end": 43125483, + "length_bp": 81189, + "mean_depth": 142.3, + "median_depth": 140.0, + "min_depth": 3, + "max_depth": 310, + "stdev_depth": 38.1, + "pct_zero": 0.12, + "pct_thresholds": { + "1": 99.9, + "5": 99.9, + "10": 99.9, + "20": 98.6, + "30": 98.6, + "50": 84.8, + "100": 71.0 + }, + "coverage_status": "PASS", + "n_lowcov_blocks": 0, + "lowcov_total_bp": 0, + "lowcov_blocks": [], + "histogram": { + "0": 96, + "30": 400, + "140": 12000 + }, + "exons": [ + { + "target_id": "BRCA1_exon1", + "contig": "chr17", + "start": 43125270, + "end": 43125483, + "length_bp": 213, + "mean_depth": 150.0, + "median_depth": 149.0, + "min_depth": 40, + "max_depth": 210, + "stdev_depth": 22.0, + "pct_zero": 0.0, + "pct_thresholds": { + "1": 100.0, + "5": 100.0, + "10": 100.0, + "20": 100.0, + "30": 100.0, + "50": 90.0, + "100": 80.0 + }, + "coverage_status": "OK", + "n_lowcov_blocks": 0, + "lowcov_total_bp": 0, + "lowcov_blocks": [], + "histogram": {}, + "exon_number": 1, + "status": "OK" + }, + { + "target_id": "BRCA1_exon2", + "contig": "chr17", + "start": 43124016, + "end": 43124114, + "length_bp": 98, + "mean_depth": 138.0, + "median_depth": 140.0, + "min_depth": 55, + "max_depth": 190, + "stdev_depth": 19.0, + "pct_zero": 0.0, + "pct_thresholds": { + "1": 100.0, + "5": 100.0, + "10": 100.0, + "20": 100.0, + "30": 100.0, + "50": 86.0, + "100": 72.0 + }, + "coverage_status": "OK", + "n_lowcov_blocks": 0, + "lowcov_total_bp": 0, + "lowcov_blocks": [], + "histogram": {}, + "exon_number": 2, + "status": "OK" + } + ] + }, + { + "target_id": "TP53", + "contig": "chr17", + "start": 7668401, + "end": 7694173, + "length_bp": 25772, + "mean_depth": 160.0, + "median_depth": 158.0, + "min_depth": 20, + "max_depth": 300, + "stdev_depth": 30.0, + "pct_zero": 0.0, + "pct_thresholds": { + "1": 100.0, + "5": 100.0, + "10": 100.0, + "20": 99.5, + "30": 99.5, + "50": 89.75, + "100": 80.0 + }, + "coverage_status": "PASS", + "n_lowcov_blocks": 0, + "lowcov_total_bp": 0, + "lowcov_blocks": [], + "histogram": { + "50": 2000, + "160": 15000 + } + } + ], + "genes": [] +} \ No newline at end of file diff --git a/data/modules/covsnap/sampleB_lowcov.covsnap.json b/data/modules/covsnap/sampleB_lowcov.covsnap.json new file mode 100644 index 00000000..98209361 --- /dev/null +++ b/data/modules/covsnap/sampleB_lowcov.covsnap.json @@ -0,0 +1,120 @@ +{ + "covsnap_version": "0.5.0", + "schema_version": "1.0", + "run": { + "sample_name": "sampleB_lowcov", + "bam_path": "/data/sampleB_lowcov.bam", + "reference": null, + "engine_used": "mosdepth", + "engine_version": "0.3.8", + "contig_style": "chr", + "run_date": "2026-06-29", + "bed_path": null, + "exon_only": false, + "thresholds": [ + 1, + 5, + 10, + 20, + 30, + 50, + 100 + ], + "classify_params": { + "pass_pct_ge_20": 95.0, + "pass_max_pct_zero": 1.0, + "dropout_pct_zero": 5.0, + "dropout_zero_block_bp": 500, + "uneven_cv": 1.0, + "exon_pct_ge_20": 90.0, + "exon_max_pct_zero": 5.0 + } + }, + "summary": { + "n_targets": 2, + "n_pass": 0, + "status_counts": { + "LOW_COVERAGE": 1, + "DROP_OUT": 1 + } + }, + "targets": [ + { + "target_id": "BRCA1", + "contig": "chr17", + "start": 43044294, + "end": 43125483, + "length_bp": 81189, + "mean_depth": 55.0, + "median_depth": 52.0, + "min_depth": 0, + "max_depth": 140, + "stdev_depth": 16.0, + "pct_zero": 4.2, + "pct_thresholds": { + "1": 96.0, + "5": 96.0, + "10": 96.0, + "20": 70.0, + "30": 70.0, + "50": 37.5, + "100": 5.0 + }, + "coverage_status": "LOW_COVERAGE", + "n_lowcov_blocks": 1, + "lowcov_total_bp": 600, + "lowcov_blocks": [ + { + "contig": "chr17", + "start": 43100000, + "end": 43100600, + "length": 600, + "mean_depth": 2.1 + } + ], + "histogram": { + "0": 3400, + "50": 40000 + } + }, + { + "target_id": "ETFDH", + "contig": "chr4", + "start": 158680400, + "end": 158716400, + "length_bp": 36000, + "mean_depth": 0.8, + "median_depth": 0.0, + "min_depth": 0, + "max_depth": 12, + "stdev_depth": 1.5, + "pct_zero": 82.0, + "pct_thresholds": { + "1": 18.0, + "5": 18.0, + "10": 18.0, + "20": 3.0, + "30": 3.0, + "50": 1.5, + "100": 0.0 + }, + "coverage_status": "DROP_OUT", + "n_lowcov_blocks": 1, + "lowcov_total_bp": 29600, + "lowcov_blocks": [ + { + "contig": "chr4", + "start": 158680400, + "end": 158710000, + "length": 29600, + "mean_depth": 0.2 + } + ], + "histogram": { + "0": 29600, + "5": 6400 + } + } + ], + "genes": [] +} \ No newline at end of file diff --git a/data/modules/covsnap/sampleC_uneven.covsnap.json b/data/modules/covsnap/sampleC_uneven.covsnap.json new file mode 100644 index 00000000..8d43947b --- /dev/null +++ b/data/modules/covsnap/sampleC_uneven.covsnap.json @@ -0,0 +1,105 @@ +{ + "covsnap_version": "0.5.0", + "schema_version": "1.0", + "run": { + "sample_name": "sampleC_uneven", + "bam_path": "/data/sampleC_uneven.bam", + "reference": null, + "engine_used": "mosdepth", + "engine_version": "0.3.8", + "contig_style": "chr", + "run_date": "2026-06-29", + "bed_path": null, + "exon_only": false, + "thresholds": [ + 1, + 5, + 10, + 20, + 30, + 50, + 100 + ], + "classify_params": { + "pass_pct_ge_20": 95.0, + "pass_max_pct_zero": 1.0, + "dropout_pct_zero": 5.0, + "dropout_zero_block_bp": 500, + "uneven_cv": 1.0, + "exon_pct_ge_20": 90.0, + "exon_max_pct_zero": 5.0 + } + }, + "summary": { + "n_targets": 2, + "n_pass": 1, + "status_counts": { + "UNEVEN": 1, + "PASS": 1 + } + }, + "targets": [ + { + "target_id": "EGFR", + "contig": "chr7", + "start": 55019016, + "end": 55211627, + "length_bp": 192611, + "mean_depth": 210.0, + "median_depth": 180.0, + "min_depth": 0, + "max_depth": 1400, + "stdev_depth": 260.0, + "pct_zero": 0.3, + "pct_thresholds": { + "1": 99.0, + "5": 99.0, + "10": 99.0, + "20": 96.0, + "30": 96.0, + "50": 78.0, + "100": 60.0 + }, + "coverage_status": "UNEVEN", + "n_lowcov_blocks": 0, + "lowcov_total_bp": 0, + "lowcov_blocks": [], + "histogram": { + "0": 600, + "180": 80000, + "1400": 200 + } + }, + { + "target_id": "KRAS", + "contig": "chr12", + "start": 25204788, + "end": 25250462, + "length_bp": 45674, + "mean_depth": 120.0, + "median_depth": 119.0, + "min_depth": 30, + "max_depth": 240, + "stdev_depth": 28.0, + "pct_zero": 0.0, + "pct_thresholds": { + "1": 100.0, + "5": 100.0, + "10": 100.0, + "20": 99.0, + "30": 99.0, + "50": 84.5, + "100": 70.0 + }, + "coverage_status": "PASS", + "n_lowcov_blocks": 0, + "lowcov_total_bp": 0, + "lowcov_blocks": [], + "histogram": { + "30": 1000, + "120": 40000 + } + } + ], + "genes": [] +} \ No newline at end of file