Mercurial > repos > jpayne > snp_pipeline

## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[samples/sample4/reads.sorted.bam] OUTPUT=samples/sample4/reads.sorted.deduped.bam METRICS_FILE=samples/sample4/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	655	9117	0	0	103	3	0	0.005771	13850242

## HISTOGRAM	java.lang.Double
BIN	VALUE
1.0	1
2.0	1.999342
3.0	2.998026
4.0	3.996053
5.0	4.993424
6.0	5.990138
7.0	6.986196
8.0	7.981599
9.0	8.976347
10.0	9.97044
11.0	10.963879
12.0	11.956665
13.0	12.948797
14.0	13.940276
15.0	14.931103
16.0	15.921277
17.0	16.9108
18.0	17.899672
19.0	18.887894
20.0	19.875465
21.0	20.862386
22.0	21.848658
23.0	22.83428
24.0	23.819255
25.0	24.803581
26.0	25.787259
27.0	26.77029
28.0	27.752674
29.0	28.734412
30.0	29.715503
31.0	30.695949
32.0	31.67575
33.0	32.654906
34.0	33.633418
35.0	34.611286
36.0	35.58851
37.0	36.565092
38.0	37.541031
39.0	38.516327
40.0	39.490982
41.0	40.464995
42.0	41.438368
43.0	42.4111
44.0	43.383191
45.0	44.354644
46.0	45.325457
47.0	46.295631
48.0	47.265166
49.0	48.234064
50.0	49.202324
51.0	50.169947
52.0	51.136933
53.0	52.103283
54.0	53.068997
55.0	54.034076
56.0	54.998519
57.0	55.962328
58.0	56.925503
59.0	57.888043
60.0	58.849951
61.0	59.811225
62.0	60.771867
63.0	61.731877
64.0	62.691255
65.0	63.650002
66.0	64.608117
67.0	65.565603
68.0	66.522458
69.0	67.478684
70.0	68.43428
71.0	69.389248
72.0	70.343587
73.0	71.297298
74.0	72.250381
75.0	73.202838
76.0	74.154668
77.0	75.105871
78.0	76.056448
79.0	77.0064
80.0	77.955727
81.0	78.904429
82.0	79.852507
83.0	80.799961
84.0	81.746791
85.0	82.692999
86.0	83.638583
87.0	84.583546
88.0	85.527887
89.0	86.471606
90.0	87.414704
91.0	88.357182
92.0	89.29904
93.0	90.240277
94.0	91.180896
95.0	92.120895
96.0	93.060276
97.0	93.999039
98.0	94.937184
99.0	95.874711
100.0	96.811622
author	jpayne
date	Wed, 24 Jan 2018 14:18:21 -0500
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