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fgbio:Adding input and output html #350

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93b5339
adding file for update in QualityByCycleMetrics to display both mean_…
Jun 11, 2025
740c0c0
adding input and output multiqc for the change
Jun 11, 2025
a4d7ae5
adding input file for picard/hsmetric.py update
Jul 30, 2025
dd49880
adding fgbio files
Jul 30, 2025
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79 changes: 79 additions & 0 deletions data/modules/fgbio/Sample1_collapsed_grouped.duplex_family_sizes.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,79 @@
ab_size ba_size count fraction fraction_gt_or_eq_size
1 0 3898545 0.589279 1
1 1 163717 0.024746 0.064372
2 0 1469639 0.222141 0.385975
2 1 126345 0.019097 0.039626
2 2 24548 0.003711 0.00958
3 0 528174 0.079835 0.141026
3 1 46385 0.007011 0.016818
3 2 18766 0.002837 0.005869
3 3 3554 0.000537 0.00139
4 0 188528 0.028497 0.050805
4 1 16702 0.002525 0.006433
4 2 6850 0.001035 0.002495
4 3 2671 0.000404 0.000853
4 4 481 0.000073 0.0002
5 0 67404 0.010188 0.018272
5 1 5970 0.000902 0.002396
5 2 2545 0.000385 0.000984
5 3 1030 0.000156 0.000377
5 4 398 0.00006 0.000127
5 5 72 0.000011 0.000029
6 0 24180 0.003655 0.00657
6 1 2155 0.000326 0.000883
6 2 948 0.000143 0.000372
6 3 388 0.000059 0.00015
6 4 143 0.000022 0.000056
6 5 56 8.4646E-6 0.000018
6 6 14 2.11615E-6 4.68576E-6
7 0 8548 0.001292 0.002355
7 1 764 0.000115 0.000323
7 2 348 0.000053 0.000138
7 3 149 0.000023 0.000059
7 4 72 0.000011 0.000024
7 5 16 2.41846E-6 7.25537E-6
7 6 8 1.20923E-6 2.56961E-6
7 7 1 1.51154E-7 4.53461E-7
8 0 3090 0.000467 0.000858
8 1 288 0.000044 0.000117
8 2 103 0.000016 0.000048
8 3 52 7.85998E-6 0.000022
8 4 24 3.62768E-6 9.37152E-6
8 5 4 6.04614E-7 3.47653E-6
8 6 2 3.02307E-7 1.20923E-6
8 7 1 1.51154E-7 3.02307E-7
9 0 1157 0.000175 0.000319
9 1 108 0.000016 0.000046
9 2 44 6.65076E-6 0.00002
9 3 19 2.87192E-6 9.22037E-6
9 4 6 9.06921E-7 4.68576E-6
9 5 8 1.20923E-6 2.41846E-6
9 6 2 3.02307E-7 7.55768E-7
10 0 392 0.000059 0.000116
10 1 42 6.34845E-6 0.000018
10 2 17 2.56961E-6 8.16229E-6
10 3 7 1.05807E-6 3.92999E-6
10 4 8 1.20923E-6 2.2673E-6
10 6 2 3.02307E-7 4.53461E-7
11 0 157 0.000024 0.000045
11 1 14 2.11615E-6 6.04614E-6
11 2 7 1.05807E-6 3.02307E-6
11 3 3 4.53461E-7 1.36038E-6
11 4 1 1.51154E-7 7.55768E-7
11 5 2 3.02307E-7 6.04614E-7
11 7 1 1.51154E-7 1.51154E-7
12 0 60 9.06921E-6 0.000017
12 1 4 6.04614E-7 1.81384E-6
12 2 2 3.02307E-7 9.06921E-7
12 5 1 1.51154E-7 1.51154E-7
13 0 27 4.08115E-6 7.25537E-6
13 1 1 1.51154E-7 7.55768E-7
14 0 4 6.04614E-7 3.02307E-6
14 2 1 1.51154E-7 4.53461E-7
14 3 1 1.51154E-7 1.51154E-7
15 0 9 1.36038E-6 2.11615E-6
15 1 1 1.51154E-7 3.02307E-7
16 0 1 1.51154E-7 6.04614E-7
16 2 1 1.51154E-7 1.51154E-7
17 0 1 1.51154E-7 3.02307E-7
23 0 1 1.51154E-7 1.51154E-7
21 changes: 21 additions & 0 deletions data/modules/fgbio/Sample1_collapsed_grouped.duplex_yield_metrics.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
fraction read_pairs cs_families ss_families ds_families ds_duplexes ds_fraction_duplexes ds_fraction_duplexes_ideal
0.05 556736 537604 541259 538667 2592 0.004812 0.016509
0.1 1113861 1039738 1053452 1043612 9840 0.009429 0.032592
0.15 1670081 1508549 1537601 1516618 20983 0.013835 0.048215
0.2 2225837 1947916 1996379 1961339 35040 0.017865 0.063261
0.25 2781076 2360167 2431928 2379948 51980 0.021841 0.077865
0.3 3337593 2748574 2846291 2775209 71082 0.025613 0.092215
0.35 3894794 3115330 3241463 3149436 92027 0.02922 0.106098
0.4 4449331 3459639 3615986 3501523 114463 0.032689 0.119583
0.45 5006303 3786738 3975049 3836925 138124 0.035999 0.132704
0.5 5562847 4096549 4317694 4155063 162631 0.03914 0.145466
0.55 6118956 4389992 4645004 4457133 187871 0.042151 0.157849
0.6 6676758 4669606 4959059 4745371 213688 0.045031 0.169949
0.65 7233533 4934984 5258996 5019158 239838 0.047785 0.181701
0.7 7788866 5186250 5545150 5278802 266348 0.050456 0.193202
0.75 8345357 5426740 5820353 5527636 292717 0.052955 0.204374
0.8 8901093 5655550 6084511 5764796 319715 0.05546 0.215273
0.85 9457394 5874154 6337738 5991642 346096 0.057763 0.225914
0.9 10014450 6083233 6581750 6208936 372814 0.060045 0.236332
0.95 10571338 6283131 6816391 6416883 399508 0.062259 0.246516
1 11127423 6474076 7041663 6615790 425873 0.064372 0.256432
21 changes: 21 additions & 0 deletions data/modules/fgbio/Sample1_collapsed_grouped.family_sizes.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
family_size cs_count cs_fraction cs_fraction_gt_or_eq_size ss_count ss_fraction ss_fraction_gt_or_eq_size ds_count ds_fraction ds_fraction_gt_or_eq_size
1 3741726 0.577955 1 4424758 0.628368 1 3898545 0.589279 1
2 1604837 0.247887 0.422045 1674712 0.237829 0.371632 1633356 0.246888 0.410721
3 662906 0.102394 0.174158 604753 0.085882 0.133803 654519 0.098933 0.163834
4 272708 0.042123 0.071764 216365 0.030726 0.04792 259461 0.039218 0.064901
5 112244 0.017337 0.029641 77578 0.011017 0.017194 102872 0.015549 0.025682
6 46542 0.007189 0.012304 27912 0.003964 0.006177 40554 0.00613 0.010133
7 19165 0.00296 0.005115 9909 0.001407 0.002213 15919 0.002406 0.004003
8 8016 0.001238 0.002154 3564 0.000506 0.000806 6313 0.000954 0.001597
9 3481 0.000538 0.000916 1344 0.000191 0.0003 2579 0.00039 0.000643
10 1393 0.000215 0.000379 468 0.000066 0.000109 967 0.000146 0.000253
11 598 0.000092 0.000163 185 0.000026 0.000043 423 0.000064 0.000107
12 273 0.000042 0.000071 67 9.5148E-6 0.000016 164 0.000025 0.000043
13 101 0.000016 0.000029 28 3.97633E-6 6.81657E-6 63 9.52267E-6 0.000018
14 50 7.72311E-6 0.000013 6 8.52071E-7 2.84024E-6 29 4.38345E-6 8.31344E-6
15 15 2.31693E-6 5.56064E-6 10 1.42012E-6 1.98817E-6 13 1.965E-6 3.92999E-6
16 8 1.2357E-6 3.24371E-6 2 2.84024E-7 5.68048E-7 7 1.05807E-6 1.965E-6
17 4 6.17849E-7 2.00801E-6 1 1.42012E-7 2.84024E-7 3 4.53461E-7 9.06921E-7
18 6 9.26773E-7 1.39016E-6 0 0 1.42012E-7 2 3.02307E-7 4.53461E-7
20 2 3.08924E-7 4.63387E-7 0 0 1.42012E-7 0 0 1.51154E-7
23 1 1.54462E-7 1.54462E-7 1 1.42012E-7 1.42012E-7 1 1.51154E-7 1.51154E-7
113 changes: 113 additions & 0 deletions data/modules/fgbio/Sample1_collapsed_grouped.umi_counts.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,113 @@
umi raw_observations raw_observations_with_errors unique_observations fraction_raw_observations fraction_unique_observations
AAA 363487 363 216738 0.016333 0.01638
AAC 354936 421 211050 0.015949 0.01595
AAG 292283 352 174547 0.013133 0.013192
AAN 828 828 413 0.000037 0.000031
AAT 580360 1116 344327 0.026078 0.026023
ACA 144693 236 86872 0.006502 0.006566
ACC 385185 501 228699 0.017308 0.017284
ACG 331507 421 197295 0.014896 0.014911
ACN 620 620 310 0.000028 0.000023
ACT 333317 577 198350 0.014977 0.014991
AGA 336093 359 200288 0.015102 0.015137
AGC 139027 159 82895 0.006247 0.006265
AGG 206203 251 123299 0.009266 0.009319
AGN 431 431 215 0.000019 0.000016
AGT 282967 317 168420 0.012715 0.012729
ANA 598 598 299 0.000027 0.000023
ANC 732 732 366 0.000033 0.000028
ANG 691 691 345 0.000031 0.000026
ANT 1634 1634 817 0.000073 0.000062
ATA 529117 602 315890 0.023775 0.023874
ATC 320665 423 190434 0.014409 0.014392
ATG 447730 649 266067 0.020118 0.020108
ATN 925 925 462 0.000042 0.000035
ATT 472476 643 280505 0.02123 0.0212
CAA 233572 241 139643 0.010495 0.010554
CAC 232419 288 137873 0.010444 0.01042
CAG 150606 189 90076 0.006767 0.006808
CAN 427 427 213 0.000019 0.000016
CAT 345448 443 205219 0.015522 0.01551
CCA 213098 352 127677 0.009575 0.009649
CCC 501579 644 297753 0.022538 0.022503
CCG 478608 650 283709 0.021506 0.021442
CCN 995 995 495 0.000045 0.000037
CCT 550471 823 327239 0.024735 0.024732
CGA 213890 231 127796 0.009611 0.009658
CGC 97976 103 58665 0.004402 0.004434
CGG 169327 174 100843 0.007609 0.007621
CGN 633 633 316 0.000028 0.000024
CGT 363769 482 217380 0.016346 0.016429
CNA 366 366 183 0.000016 0.000014
CNC 584 584 291 0.000026 0.000022
CNG 599 599 299 0.000027 0.000023
CNT 894 894 447 0.00004 0.000034
CTA 289456 387 172155 0.013006 0.013011
CTC 343161 464 203989 0.01542 0.015417
CTG 467467 683 276381 0.021005 0.020888
CTN 717 717 358 0.000032 0.000027
CTT 433538 620 256923 0.019481 0.019417
GAA 288987 380 173143 0.012985 0.013086
GAC 356447 445 211733 0.016017 0.016002
GAG 297045 349 176707 0.013347 0.013355
GAN 880 880 440 0.00004 0.000033
GAT 442464 582 263312 0.019882 0.0199
GCA 193977 338 116155 0.008716 0.008779
GCC 329066 381 195302 0.014786 0.01476
GCG 243539 212 144686 0.010943 0.010935
GCN 691 691 345 0.000031 0.000026
GCT 367588 465 218914 0.016517 0.016545
GGA 306360 340 183393 0.013766 0.01386
GGC 232356 238 138667 0.010441 0.01048
GGG 315838 263 188159 0.014192 0.01422
GGN 1144 1144 571 0.000051 0.000043
GGT 436644 574 260022 0.01962 0.019652
GNA 730 730 364 0.000033 0.000028
GNC 979 979 489 0.000044 0.000037
GNG 1008 1008 504 0.000045 0.000038
GNT 2127 2127 1061 0.000096 0.00008
GTA 340266 525 203156 0.01529 0.015354
GTC 308144 370 182874 0.013846 0.013821
GTG 388624 466 230606 0.017462 0.017428
GTN 1002 1002 501 0.000045 0.000038
GTT 676881 1307 401169 0.030415 0.030319
NAA 958 958 479 0.000043 0.000036
NAC 926 926 463 0.000042 0.000035
NAG 778 778 388 0.000035 0.000029
NAT 1714 1714 856 0.000077 0.000065
NCA 826 826 413 0.000037 0.000031
NCC 1533 1533 766 0.000069 0.000058
NCG 1375 1375 687 0.000062 0.000052
NCT 1750 1750 874 0.000079 0.000066
NGA 922 922 461 0.000041 0.000035
NGC 516 516 258 0.000023 0.000019
NGG 1039 1039 518 0.000047 0.000039
NGT 1344 1344 672 0.00006 0.000051
NTA 2200 2200 1099 0.000099 0.000083
NTC 1612 1612 805 0.000072 0.000061
NTG 2732 2732 1364 0.000123 0.000103
NTT 2618 2618 1308 0.000118 0.000099
TAA 408839 604 244090 0.018371 0.018448
TAC 320058 425 190667 0.014381 0.01441
TAG 250988 428 149547 0.011278 0.011302
TAN 858 858 428 0.000039 0.000032
TAT 553535 1069 328280 0.024873 0.02481
TCA 294971 435 175361 0.013254 0.013253
TCC 401718 489 237415 0.018051 0.017943
TCG 287826 415 171228 0.012933 0.012941
TCN 708 708 354 0.000032 0.000027
TCT 457175 546 270964 0.020543 0.020479
TGA 553271 608 328484 0.024861 0.024826
TGC 169812 205 100407 0.00763 0.007588
TGG 288971 462 171696 0.012985 0.012976
TGN 824 824 411 0.000037 0.000031
TGT 486113 644 288073 0.021843 0.021772
TNA 688 688 344 0.000031 0.000026
TNC 516 516 258 0.000023 0.000019
TNG 542 542 271 0.000024 0.00002
TNT 861 861 430 0.000039 0.000032
TTA 414674 984 248743 0.018633 0.018799
TTC 273702 572 162261 0.012299 0.012263
TTG 395176 952 234183 0.017757 0.017699
TTN 760 760 379 0.000034 0.000029
TTT 520525 1284 308796 0.023389 0.023338
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