Mercurial > repos > jpayne > snp_pipeline

## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[samples/sample3/reads.sorted.bam] OUTPUT=samples/sample3/reads.sorted.deduped.bam METRICS_FILE=samples/sample3/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 20:46:32 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	692	9097	0	0	114	2	0	0.006248	20685819

## HISTOGRAM	java.lang.Double
BIN	VALUE
1.0	1
2.0	1.99956
3.0	2.998681
4.0	3.997363
5.0	4.995605
6.0	5.993409
7.0	6.990774
8.0	7.9877
9.0	8.984188
10.0	9.980238
11.0	10.97585
12.0	11.971024
13.0	12.965761
14.0	13.96006
15.0	14.953922
16.0	15.947347
17.0	16.940336
18.0	17.932887
19.0	18.925003
20.0	19.916682
21.0	20.907925
22.0	21.898733
23.0	22.889104
24.0	23.879041
25.0	24.868542
26.0	25.857608
27.0	26.846239
28.0	27.834435
29.0	28.822197
30.0	29.809525
31.0	30.796418
32.0	31.782878
33.0	32.768904
34.0	33.754496
35.0	34.739655
36.0	35.724381
37.0	36.708674
38.0	37.692534
39.0	38.675962
40.0	39.658957
41.0	40.64152
42.0	41.623651
43.0	42.60535
44.0	43.586618
45.0	44.567454
46.0	45.547859
47.0	46.527833
48.0	47.507376
49.0	48.486488
50.0	49.46517
51.0	50.443421
52.0	51.421243
53.0	52.398634
54.0	53.375596
55.0	54.352128
56.0	55.328231
57.0	56.303904
58.0	57.279149
59.0	58.253965
60.0	59.228352
61.0	60.202311
62.0	61.175842
63.0	62.148945
64.0	63.121619
65.0	64.093866
66.0	65.065686
67.0	66.037078
68.0	67.008044
69.0	67.978582
70.0	68.948694
71.0	69.918379
72.0	70.887638
73.0	71.85647
74.0	72.824877
75.0	73.792858
76.0	74.760413
77.0	75.727543
78.0	76.694247
79.0	77.660527
80.0	78.626382
81.0	79.591812
82.0	80.556817
83.0	81.521399
84.0	82.485556
85.0	83.449289
86.0	84.412599
87.0	85.375485
88.0	86.337948
89.0	87.299987
90.0	88.261604
91.0	89.222797
92.0	90.183569
93.0	91.143917
94.0	92.103844
95.0	93.063348
96.0	94.022431
97.0	94.981092
98.0	95.939331
99.0	96.897149
100.0	97.854546
author	jpayne
date	Wed, 24 Jan 2018 14:18:21 -0500
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