Mercurial > repos > jpayne > snp_pipeline

## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[samples/sample2/reads.sorted.bam] OUTPUT=samples/sample2/reads.sorted.deduped.bam METRICS_FILE=samples/sample2/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	614	9171	0	0	92	3	0	0.00517	14014816

## HISTOGRAM	java.lang.Double
BIN	VALUE
1.0	1
2.0	1.999346
3.0	2.998038
4.0	3.996077
5.0	4.993463
6.0	5.990196
7.0	6.986278
8.0	7.981707
9.0	8.976486
10.0	9.970614
11.0	10.964091
12.0	11.956919
13.0	12.949097
14.0	13.940626
15.0	14.931507
16.0	15.921739
17.0	16.911324
18.0	17.900261
19.0	18.888551
20.0	19.876195
21.0	20.863193
22.0	21.849545
23.0	22.835252
24.0	23.820314
25.0	24.804731
26.0	25.788505
27.0	26.771635
28.0	27.754122
29.0	28.735966
30.0	29.717168
31.0	30.697728
32.0	31.677647
33.0	32.656924
34.0	33.635561
35.0	34.613558
36.0	35.590915
37.0	36.567633
38.0	37.543712
39.0	38.519152
40.0	39.493954
41.0	40.468118
42.0	41.441646
43.0	42.414536
44.0	43.38679
45.0	44.358408
46.0	45.32939
47.0	46.299737
48.0	47.269449
49.0	48.238527
50.0	49.206971
51.0	50.174782
52.0	51.141959
53.0	52.108504
54.0	53.074417
55.0	54.039697
56.0	55.004346
57.0	55.968364
58.0	56.931752
59.0	57.894509
60.0	58.856637
61.0	59.818135
62.0	60.779004
63.0	61.739244
64.0	62.698857
65.0	63.657841
66.0	64.616198
67.0	65.573929
68.0	66.531033
69.0	67.48751
70.0	68.443362
71.0	69.398589
72.0	70.353191
73.0	71.307168
74.0	72.260522
75.0	73.213252
76.0	74.165358
77.0	75.116842
78.0	76.067703
79.0	77.017942
80.0	77.96756
81.0	78.916556
82.0	79.864931
83.0	80.812687
84.0	81.759822
85.0	82.706337
86.0	83.652234
87.0	84.597512
88.0	85.542171
89.0	86.486212
90.0	87.429636
91.0	88.372442
92.0	89.314632
93.0	90.256206
94.0	91.197163
95.0	92.137505
96.0	93.077232
97.0	94.016344
98.0	94.954842
99.0	95.892726
100.0	96.829996
author	jpayne
date	Wed, 24 Jan 2018 14:18:21 -0500
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