## htsjdk.samtools.metrics.StringHeader
# au.edu.wehi.idsv.Idsv INPUT=[/mnt/bam/CPCG0100/CPCG0100R/CPCG_0100_Ly_R_PE_469_WG_120201_h803_0081_BC0GHHACXX_7_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100R/CPCG_0100_Ly_R_PE_469_WG_120201_h803_0081_BC0GHHACXX_8_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100R/CPCG_0100_Ly_R_PE_469_WG_120201_h803_0080_AD0JHUACXX_8_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100R/CPCG_0100_Ly_R_PE_469_WG_120201_h803_0080_AD0JHUACXX_7_NoIndex.markdup.bam] INPUT_TUMOUR=[/mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_3_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_6_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_5_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_2_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_4_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_1_NoIndex.markdup.bam] OUTPUT=/mnt/bam/CPCG0100/CPCG0100.vcf REFERENCE=/mnt/reference/hg19/hg19_random.fa SCRIPT=/mnt/bam/CPCG0100/gridss/realign.sh PER_CHR=true WORKING_DIR=/mnt/bam/CPCG0100/gridss CALL_ONLY_ASSEMBLIES=true TMP_DIR=[/mnt/bam/CPCG0100/gridss] VERBOSITY=DEBUG    STEPS=[CALCULATE_METRICS, EXTRACT_SOFT_CLIPS, EXTRACT_READ_PAIRS, ASSEMBLE_BREAKENDS, REALIGN_SOFT_CLIPS, REALIGN_ASSEMLIES, SORT_REALIGNED_SOFT_CLIPS, SORT_REALIGNED_ASSEMBLIES, CALL_STRUCTURAL_VARIANTS, ANNOTATE_VARIANTS] SOFT_CLIP_MIN_LENGTH=4 READ_PAIR_ANCHOR_MIN_MAPQ=5 SOFT_CLIP_MIN_MAPQ=5 SOFT_CLIP_MIN_ANCHOR_PERCENT_IDENTITY=95.0 ASSEMBLY_METHOD=DEBRUIJN_SUBGRAPH ASSEMBLY_DEBRUIJN_KMER=25 ASSEMBLY_DEBRUIJN_MAX_PATH_COLLAPSE_BASE_MISMATCHES=2 ASSEMBLY_DEBRUIJN_COLLAPSE_BUBBLES_ONLY=false ASSEMBLY_DEBRUIJN_ALLOW_REFERENCE_KMER_RESUSE=true ASSEMBLY_DEBRUIJN_MAX_CONTIGS_PER_ITERATION=1024 ASSEMBLY_DEBRUIJN_SUBGRAPH_BRANCHING_FACTOR=16 ASSEMBLY_DEBRUIJN_SUBGRAPH_ASSEMBLY_FRAGMENT_DELAY=3.0 REALIGNMENT_MIN_BREAKEND_LENGTH=20 REALIGNMENT_MIN_BASE_QUALITY=5.0 REALIGNMENT_MAPQ_UNIQUE_THRESHOLD=10 SOMATIC_THRESHOLD=0.001 MIN_INDEL_SIZE=16 VCF41_COMPATIBLE=true QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Oct 29 03:01:08 UTC 2014

## METRICS CLASS	picard.analysis.InsertSizeMetrics
MEDIAN_INSERT_SIZE	MEDIAN_ABSOLUTE_DEVIATION	MIN_INSERT_SIZE	MAX_INSERT_SIZE	MEAN_INSERT_SIZE	STANDARD_DEVIATION	READ_PAIRS	PAIR_ORIENTATION	WIDTH_OF_10_PERCENT	WIDTH_OF_20_PERCENT	WIDTH_OF_30_PERCENT	WIDTH_OF_40_PERCENT	WIDTH_OF_50_PERCENT	WIDTH_OF_60_PERCENT	WIDTH_OF_70_PERCENT	WIDTH_OF_80_PERCENT	WIDTH_OF_90_PERCENT	WIDTH_OF_99_PERCENT	SAMPLE	LIBRARY	READ_GROUP
185	47	23	203426909	202.883466	78.486411	188545117	FR	19	37	57	75	95	117	139	163	255	537			

## HISTOGRAM	java.lang.Integer
insert_size	All_Reads.fr_count
23	8
24	4
25	178
26	141
27	322
28	213
29	555
30	368
31	729
32	550
33	762
34	667
35	984
36	892
37	1218
38	1117
39	1698
40	1299
41	1960
42	1475
43	2214
44	1726
45	2393
46	1909
47	2293
48	2033
49	2524
50	2154
51	2724
52	2508
53	3304
54	2656
55	3493
56	2913
57	3765
58	3149
59	4126
60	3381
61	3830
62	3386
63	4090
64	3800
65	4369
66	4148
67	5006
68	4259
69	5305
70	4455
71	5416
72	4854
73	5875
74	5134
75	5814
76	5464
77	6283
78	5825
79	6602
80	6273
81	7490
82	6837
83	7951
84	7498
85	8692
86	8215
87	9473
88	8969
89	10006
90	9996
91	11170
92	11097
93	12616
94	12842
95	14874
96	15299
97	17978
98	20084
99	24720
100	31393
101	396477
102	916277
103	937420
104	960603
105	972647
106	982051
107	996117
108	1008493
109	1020274
110	1031511
111	1043874
112	1048597
113	1057284
114	1062855
115	1071322
116	1078094
117	1083226
118	1091496
119	1095515
120	1101033
121	1106335
122	1111626
123	1116359
124	1119446
125	1123163
126	1125995
127	1131946
128	1135021
129	1140964
130	1144127
131	1149267
132	1153618
133	1158294
134	1163123
135	1167165
136	1171886
137	1174558
138	1175405
139	1181310
140	1183939
141	1185453
142	1189435
143	1192352
144	1195246
145	1193985
146	1194953
147	1194648
148	1196355
149	1197245
150	1195575
151	1194357
152	1193528
153	1191588
154	1192340
155	1188691
156	1187164
157	1186207
158	1182506
159	1180687
160	1176851
161	1171793
162	1168158
163	1164122
164	1161368
165	1157729
166	1152185
167	1149117
168	1144606
169	1139335
170	1132014
171	1125108
172	1117224
173	1113050
174	1105538
175	1102149
176	1094382
177	1088286
178	1080916
179	1075036
180	1065181
181	1057749
182	1050487
183	1043562
184	1036105
185	1028003
186	1022690
187	1016218
188	1007748
189	1001591
190	993292
191	985512
192	977442
193	968603
194	960001
195	952356
196	945258
197	937166
198	929437
199	925008
200	915445
201	906690
202	898113
203	891216
204	883284
205	876634
206	868312
207	860305
208	853017
209	844145
210	837690
211	829813
212	822254
213	813048
214	805120
215	797790
216	790292
217	784500
218	773589
219	769743
220	761147
221	754680
222	745682
223	737549
224	731654
225	721367
226	715228
227	709177
228	701330
229	694152
230	687856
231	682126
232	673855
233	667868
234	658426
235	651732
236	644948
237	637922
238	630500
239	624134
240	620157
241	612311
242	605867
243	599134
244	593034
245	586065
246	579196
247	572250
248	566223
249	559702
250	553463
251	548504
252	543111
253	535743
254	529636
255	524166
256	516687
257	512220
258	505933
259	501069
260	494932
261	490426
262	484205
263	479402
264	474096
265	466138
266	461134
267	456809
268	451691
269	447137
270	442044
271	438757
272	434083
273	427692
274	421768
275	416441
276	410235
277	405638
278	399733
279	395903
280	391584
281	386471
282	383031
283	378358
284	374593
285	368753
286	362981
287	358966
288	354104
289	350442
290	346863
291	343100
292	339382
293	334784
294	330434
295	325403
296	322027
297	317789
298	312873
299	309696
300	306785
301	301994
302	298822
303	293987
304	291969
305	288721
306	283575
307	280773
308	276286
309	273833
310	270118
311	266209
312	262357
313	259829
314	256297
315	254077
316	250293
317	246809
318	243897
319	240966
320	238015
321	234317
322	231810
323	229198
324	226514
325	223531
326	220449
327	216955
328	214125
329	210937
330	208552
331	206274
332	203076
333	200770
334	198462
335	195653
336	193753
337	191058
338	187989
339	185871
340	183114
341	180312
342	178559
343	176892
344	173245
345	171911
346	169037
347	166271
348	164958
349	162810
350	160713
351	158531
352	156641
353	154513
354	152419
355	149747
356	148388
357	145701
358	144095
359	143432
360	140729
361	137910
362	136370
363	135182
364	132788
365	131728
366	129608
367	128826
368	126011
369	124326
370	123029
371	121318
372	120057
373	117362
374	116788
375	114611
376	113382
377	111718
378	110461
379	108599
380	106879
381	105909
382	105102
383	102924
384	101962
385	100327
386	98679
387	97474
388	96759
389	94878
390	93782
391	92198
392	91094
393	89748
394	89446
395	87886
396	86431
397	84942
398	83748
399	83013
400	81733
401	80764
402	79776
403	78768
404	77916
405	76752
406	75259
407	74549
408	73564
409	72529
410	70943
411	70126
412	69463
413	68457
414	68007
415	66755
416	65585
417	64952
418	64172
419	62992
420	62646
421	61185
422	60767
423	60227
424	58621
425	58734
426	57583
427	56487
428	55893
429	55598
430	54674
431	53981
432	53227
433	52688
434	52266
435	51712
436	52325
437	52781
438	54657
439	54837
440	55874
441	54275
442	53259
443	51357
444	47076
445	45646
446	44440
447	43545
448	42789
449	42779
450	41692
451	41220
452	40650
453	40535
454	39482
455	38833
456	38767
457	38263
458	37840
459	37018
460	36914
461	36270
462	35933
463	35312
464	34868
465	34745
466	34306
467	33633
468	33125
469	32882
470	32667
471	32331
472	31843
473	31466
474	31180
475	30755
476	30275
477	29966
478	29843
479	29506
480	29610
481	28863
482	28751
483	28405
484	28071
485	27740
486	27789
487	26900
488	27249
489	26805
490	26478
491	26314
492	26110
493	25345
494	25545
495	25566
496	25247
497	24970
498	24560
499	24755
500	24833
501	12094
502	10947
503	10078
504	9286
505	9006
506	8580
507	8103
508	7957
509	7892
510	7609
511	7413
512	7238
513	6970
514	6560
515	6526
516	6344
517	6244
518	6042
519	6066
520	5844
521	5654
522	5445
523	5485
524	5284
525	5126
526	4986
527	4853
528	4774
529	4803
530	4540
531	4462
532	4436
533	4331
534	4256
535	4084
536	3974
537	3986
538	3932
539	3851
540	3909
541	3892
542	3928
543	4249
544	4437
545	4583
546	5431
547	7132
548	10402
549	14779
550	18275
551	3011
552	2407
553	1822
554	1681
555	1572
556	1496
557	1462
558	1352
559	1248
560	1329
561	1223
562	1251
563	1181
564	1079
565	1154
566	1129
567	1099
568	1111
569	965
570	970
571	871
572	952
573	919
574	869
575	855
576	829
577	822
578	857
579	831
580	775
581	791
582	782
583	795
584	674
585	741
586	699
587	664
588	664
589	650
590	664
591	673
592	599
593	625
594	653
595	611
596	592
597	578
598	571
599	563
600	604
601	610
602	838
603	999
604	1043
605	956
606	960
607	946
608	921
609	900
610	882
611	863
612	860
613	849
614	884
615	842
616	808
617	833
618	796
619	756
620	762
621	760
622	723
623	724
624	712
625	725
626	670
627	639
628	611
629	633
630	624
631	597
632	607
633	631
634	621
635	549
636	608
637	557
638	606
639	553
640	532
641	523
642	542
643	486
644	470
645	528
646	470
647	449
648	445
649	444
650	391
651	403
652	390
653	414
654	374
655	383

