## htsjdk.samtools.metrics.StringHeader
# CollectHsMetrics BAIT_INTERVALS=[in/baits.interval_list] TARGET_INTERVALS=[in/targets.interval_list] INPUT=in/sample.bam OUTPUT=picard/hs.hs_metrics PER_TARGET_COVERAGE=picard/hs.per_target_coverage.txt PER_BASE_COVERAGE=picard/hs.per_base_coverage.txt REFERENCE_SEQUENCE=in/reference.shifted.for.crams.fasta    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true INCLUDE_INDELS=false COVERAGE_CAP=200 SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Oct 24 21:42:22 HST 2026

## METRICS CLASS	picard.analysis.directed.HsMetrics
BAIT_SET	BAIT_TERRITORY	BAIT_DESIGN_EFFICIENCY	ON_BAIT_BASES	NEAR_BAIT_BASES	OFF_BAIT_BASES	PCT_SELECTED_BASES	PCT_OFF_BAIT	ON_BAIT_VS_SELECTED	MEAN_BAIT_COVERAGE	PCT_USABLE_BASES_ON_BAIT	PCT_USABLE_BASES_ON_TARGET	FOLD_ENRICHMENT	HS_LIBRARY_SIZE	HS_PENALTY_10X	HS_PENALTY_20X	HS_PENALTY_30X	HS_PENALTY_40X	HS_PENALTY_50X	HS_PENALTY_100X	TARGET_TERRITORY	GENOME_SIZE	TOTAL_READS	PF_READS	PF_BASES	PF_UNIQUE_READS	PF_UQ_READS_ALIGNED	PF_BASES_ALIGNED	PF_UQ_BASES_ALIGNED	ON_TARGET_BASES	PCT_PF_READS	PCT_PF_UQ_READS	PCT_PF_UQ_READS_ALIGNED	MEAN_TARGET_COVERAGE	MEDIAN_TARGET_COVERAGE	MAX_TARGET_COVERAGE	MIN_TARGET_COVERAGE	ZERO_CVG_TARGETS_PCT	PCT_EXC_DUPE	PCT_EXC_ADAPTER	PCT_EXC_MAPQ	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_OFF_TARGET	FOLD_80_BASE_PENALTY	PCT_TARGET_BASES_1X	PCT_TARGET_BASES_2X	PCT_TARGET_BASES_10X	PCT_TARGET_BASES_20X	PCT_TARGET_BASES_30X	PCT_TARGET_BASES_40X	PCT_TARGET_BASES_50X	PCT_TARGET_BASES_100X	PCT_TARGET_BASES_250X	PCT_TARGET_BASES_500X	PCT_TARGET_BASES_1000X	PCT_TARGET_BASES_2500X	PCT_TARGET_BASES_5000X	PCT_TARGET_BASES_10000X	PCT_TARGET_BASES_25000X	PCT_TARGET_BASES_50000X	PCT_TARGET_BASES_100000X	AT_DROPOUT	GC_DROPOUT	HET_SNP_SENSITIVITY	HET_SNP_Q	SAMPLE	LIBRARY	READ_GROUP
baits	1000	0.5	83363	63742	0	1	0	0.56669	83.363	0.56105	0.237374	3.402976	14903	4.604988	4.619319	4.631262	4.640816	4.658013	4.715338	500	6005	984	984	148584	968	965	147105	144692	35270	1	0.98374	0.996901	70.54	71	94	35	0	0.016403	0	0	0.065028	0.069631	0.609177	1.119683	1	1	1	1	1	0.966	0.926	0	0	0	0	0	0	0	0	0	0	4.360646	0	1	73			

## HISTOGRAM	java.lang.Integer
coverage_or_base_quality	high_quality_coverage_count	unfiltered_baseq_count
0	0	0
1	0	0
2	0	0
3	0	13
4	0	19
5	0	44
6	0	59
7	0	86
8	0	100
9	0	109
10	0	103
11	0	146
12	0	141
13	0	161
14	0	131
15	0	126
16	0	156
17	0	145
18	0	111
19	0	139
20	0	153
21	0	188
22	0	302
23	0	443
24	0	557
25	0	627
26	0	935
27	0	1750
28	0	5639
29	0	10994
30	0	8134
31	0	4105
32	0	1238
33	0	202
34	0	3
35	2	0
36	2	0
37	4	0
38	6	0
39	3	0
40	1	0
41	3	0
42	1	0
43	0	0
44	4	0
45	4	0
46	0	0
47	6	0
48	0	0
49	1	0
50	0	0
51	1	0
52	2	0
53	1	0
54	0	0
55	3	0
56	4	0
57	7	0
58	4	0
59	10	0
60	5	0
61	7	0
62	13	0
63	8	0
64	9	0
65	15	0
66	18	0
67	22	0
68	16	0
69	26	0
70	31	0
71	32	0
72	20	0
73	22	0
74	16	0
75	18	0
76	14	0
77	10	0
78	9	0
79	14	0
80	4	0
81	5	0
82	10	0
83	10	0
84	10	0
85	9	0
86	7	0
87	15	0
88	9	0
89	7	0
90	7	0
91	6	0
92	2	0
93	3	0
94	2	0
95	0	0
96	0	0
97	0	0
98	0	0
99	0	0
100	0	0
101	0	0
102	0	0
103	0	0
104	0	0
105	0	0
106	0	0
107	0	0
108	0	0
109	0	0
110	0	0
111	0	0
112	0	0
113	0	0
114	0	0
115	0	0
116	0	0
117	0	0
118	0	0
119	0	0
120	0	0
121	0	0
122	0	0
123	0	0
124	0	0
125	0	0
126	0	0

