## htsjdk.samtools.metrics.StringHeader
# CollectTargetedPcrMetrics AMPLICON_INTERVALS=in/baits.interval_list TARGET_INTERVALS=[in/targets.interval_list] INPUT=in/sample.bam OUTPUT=picard/pcr.targeted_pcr_metrics REFERENCE_SEQUENCE=in/reference.shifted.for.crams.fasta    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false 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 21:42:29 HST 2026

## METRICS CLASS	picard.analysis.directed.TargetedPcrMetrics
CUSTOM_AMPLICON_SET	AMPLICON_TERRITORY	ON_AMPLICON_BASES	NEAR_AMPLICON_BASES	OFF_AMPLICON_BASES	PCT_AMPLIFIED_BASES	PCT_OFF_AMPLICON	ON_AMPLICON_VS_SELECTED	MEAN_AMPLICON_COVERAGE	FOLD_ENRICHMENT	PF_SELECTED_PAIRS	PF_SELECTED_UNIQUE_PAIRS	ON_TARGET_FROM_PAIR_BASES	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	83363	63742	0	1	0	0.56669	83.363	3.402976	491	483	40504	500	6005	984	984	148584	968	965	147105	144692	40639	1	0.98374	0.996901	78.694	78	105	39	0	0.016403	0	0	0	0	0.707338	1.108366	1	1	1	1	1	0.998	0.954	0.032	0	0	0	0	0	0	0	0	0	4.28851	0	1	78			

## 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	14
4	0	21
5	0	45
6	0	63
7	0	88
8	0	108
9	0	117
10	0	110
11	0	149
12	0	149
13	0	174
14	0	146
15	0	137
16	0	166
17	0	154
18	0	117
19	0	144
20	0	163
21	0	204
22	0	324
23	0	475
24	0	601
25	0	675
26	0	998
27	0	1850
28	0	5804
29	0	11432
30	0	8738
31	0	4542
32	0	1391
33	0	244
34	0	4
35	0	0
36	0	0
37	0	0
38	0	0
39	1	0
40	0	0
41	3	0
42	5	0
43	5	0
44	4	0
45	3	0
46	1	0
47	0	0
48	0	0
49	1	0
50	1	0
51	6	0
52	4	0
53	3	0
54	0	0
55	1	0
56	0	0
57	1	0
58	0	0
59	2	0
60	1	0
61	0	0
62	1	0
63	0	0
64	3	0
65	2	0
66	2	0
67	5	0
68	8	0
69	12	0
70	15	0
71	21	0
72	12	0
73	10	0
74	17	0
75	21	0
76	29	0
77	32	0
78	32	0
79	28	0
80	18	0
81	13	0
82	19	0
83	6	0
84	3	0
85	6	0
86	3	0
87	9	0
88	13	0
89	6	0
90	8	0
91	9	0
92	4	0
93	4	0
94	10	0
95	15	0
96	12	0
97	13	0
98	13	0
99	8	0
100	6	0
101	6	0
102	1	0
103	0	0
104	2	0
105	1	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

