Mercurial > repos > jpayne > snp_pipeline

## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[samples/sample1/reads.sorted.bam] OUTPUT=samples/sample1/reads.sorted.deduped.bam METRICS_FILE=samples/sample1/duplicate_reads_metrics.txt VERBOSITY=WARNING    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Jan 03 20:46:11 UTC 2018

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	647	9131	0	0	106	2	0	0.005817	20840746

## HISTOGRAM	java.lang.Double
BIN	VALUE
1.0	1
2.0	1.999562
3.0	2.998686
4.0	3.997373
5.0	4.995622
6.0	5.993433
7.0	6.990808
8.0	7.987746
9.0	8.984247
10.0	9.980311
11.0	10.97594
12.0	11.971132
13.0	12.965888
14.0	13.960208
15.0	14.954093
16.0	15.947543
17.0	16.940557
18.0	17.933137
19.0	18.925281
20.0	19.916991
21.0	20.908267
22.0	21.899109
23.0	22.889516
24.0	23.879489
25.0	24.869029
26.0	25.858136
27.0	26.846809
28.0	27.835049
29.0	28.822856
30.0	29.810231
31.0	30.797173
32.0	31.783683
33.0	32.76976
34.0	33.755406
35.0	34.74062
36.0	35.725402
37.0	36.709753
38.0	37.693673
39.0	38.677162
40.0	39.66022
41.0	40.642847
42.0	41.625044
43.0	42.606811
44.0	43.588148
45.0	44.569054
46.0	45.549532
47.0	46.529579
48.0	47.509198
49.0	48.488387
50.0	49.467147
51.0	50.445479
52.0	51.423382
53.0	52.400857
54.0	53.377903
55.0	54.354522
56.0	55.330712
57.0	56.306476
58.0	57.281811
59.0	58.25672
60.0	59.231201
61.0	60.205256
62.0	61.178884
63.0	62.152085
64.0	63.12486
65.0	64.097209
66.0	65.069132
67.0	66.04063
68.0	67.011702
69.0	67.982348
70.0	68.952569
71.0	69.922366
72.0	70.891737
73.0	71.860684
74.0	72.829206
75.0	73.797305
76.0	74.764979
77.0	75.732229
78.0	76.699055
79.0	77.665459
80.0	78.631438
81.0	79.596995
82.0	80.562128
83.0	81.526839
84.0	82.491128
85.0	83.454994
86.0	84.418437
87.0	85.381459
88.0	86.344059
89.0	87.306237
90.0	88.267994
91.0	89.229329
92.0	90.190243
93.0	91.150737
94.0	92.11081
95.0	93.070462
96.0	94.029693
97.0	94.988505
98.0	95.946897
99.0	96.904868
100.0	97.862421
author	jpayne
date	Thu, 01 Feb 2018 19:01:35 -0500
parents	eefdd97a6749
children