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Merged
rhshah merged 3 commits into from
Jul 24, 2017
Merged

Merge from rhshah/master #9

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36b19f8
Merge pull request #2 from mskcc/rhshah-patch-1
rhshah May 3, 2017
9376aed
Merge pull request #3 from mskcc/master
rhshah May 4, 2017
66b88c0
Multiple Changes
rhshah Jul 24, 2017
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250 changes: 250 additions & 0 deletions data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.txt
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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,258 @@
PoolTumor2-T 1 658776 GCAC G .
PoolTumor2-T 1 16200729 A ATT .
PoolTumor2-T 1 16245610 GT G .
PoolTumor2-T 1 16975201 CT C .
PoolTumor2-T 1 17085254 GA G .
PoolTumor2-T 1 17354373 G GGAAGAA .
PoolTumor2-T 1 19043478 C CG .
PoolTumor2-T 1 78414402 GT G .
PoolTumor2-T 1 85733704 TA T .
PoolTumor2-T 1 118161094 GTC G .
PoolTumor2-T 1 148643701 AAAAC A .
PoolTumor2-T 1 148873257 CT C .
PoolTumor2-T 1 150849071 AC A .
PoolTumor2-T 1 167509623 T TAGC .
PoolTumor2-T 1 170778488 CA C .
PoolTumor2-T 1 180810249 GT G .
PoolTumor2-T 1 188263961 AACAC A .
PoolTumor2-T 1 193121496 C CT .
PoolTumor2-T 1 201189188 C CT .
PoolTumor2-T 1 209812969 TACACAC T .
PoolTumor2-T 1 229106423 C CTG .
PoolTumor2-T 1 230331593 G GT .
PoolTumor2-T 1 240683382 A AAAAATAAAAT .
PoolTumor2-T 2 6636086 A AGCTTCGTTAAACTTCACTCGGAAGT .
PoolTumor2-T 2 29451557 GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G .
PoolTumor2-T 2 29451675 A AGGGCG .
PoolTumor2-T 2 44561591 C CA .
PoolTumor2-T 2 47096644 ATTGT A .
PoolTumor2-T 2 48033272 ATTTTTGTTTTAATTCCT A .
PoolTumor2-T 2 48033546 C CT .
PoolTumor2-T 2 48033846 CAGTAAA C .
PoolTumor2-T 2 51288511 T TACACACACACACACAC .
PoolTumor2-T 2 51288525 C CACACACACACACAT .
PoolTumor2-T 2 79423062 TTTTG T .
PoolTumor2-T 2 91902876 CAT C .
PoolTumor2-T 2 103352305 G GCA .
PoolTumor2-T 2 106021465 ACT A .
PoolTumor2-T 2 111878556 TGCCGCCGCCGCC T .
PoolTumor2-T 2 117248834 T TG .
PoolTumor2-T 2 134775262 CAAA C .
PoolTumor2-T 2 144383034 T TTGC .
PoolTumor2-T 2 204637705 TTCATCATCATCA T .
PoolTumor2-T 2 209102117 A ACT .
PoolTumor2-T 2 209103969 G GA .
PoolTumor2-T 2 236253185 TCTCACACAGGCACA T .
PoolTumor2-T 2 239604413 TA T .
PoolTumor2-T 2 241405400 C CGTG .
PoolTumor2-T 3 37092173 GTTC G .
PoolTumor2-T 3 47103861 G GTT .
PoolTumor2-T 3 49725284 CT C .
PoolTumor2-T 3 52620628 GT G .
PoolTumor2-T 3 113802161 CTGT C .
PoolTumor2-T 3 138423181 CAT C .
PoolTumor2-T 3 142215120 CTATATATATATATATA C .
PoolTumor2-T 3 158104615 CAAA C .
PoolTumor2-T 3 189507518 C CAG .
PoolTumor2-T 3 194317814 T TGCGTGCACACACCCACATGCACAC .
PoolTumor2-T 3 195717078 G GGCGCCAG .
PoolTumor2-T 3 195717081 C CGCGCCAG .
PoolTumor2-T 3 197951869 CGGT C .
PoolTumor2-T 4 1809127 CGTGT C .
PoolTumor2-T 4 8043638 G GAA .
PoolTumor2-T 4 38018679 T TG .
PoolTumor2-T 4 55953747 CG C .
PoolTumor2-T 4 55965031 AT A .
PoolTumor2-T 4 66286113 G GAA .
PoolTumor2-T 4 66286113 G GAAA .
PoolTumor2-T 4 95616928 C CT .
PoolTumor2-T 4 116539618 C CGA .
PoolTumor2-T 4 136777565 CT C .
PoolTumor2-T 4 144106031 T TC .
PoolTumor2-T 5 14971859 C CAA .
PoolTumor2-T 5 37744444 GA G .
PoolTumor2-T 5 52074533 C CTGT .
PoolTumor2-T 5 52665229 GTCT AGAC .
PoolTumor2-T 5 57752811 CA C .
PoolTumor2-T 5 57754489 ACT A .
PoolTumor2-T 5 86669949 A AAT .
PoolTumor2-T 5 112164716 C CT .
PoolTumor2-T 5 112213678 CTGTGTG C .
PoolTumor2-T 5 112213678 CTGTGTGTG C .
PoolTumor2-T 5 149497110 C CCA .
PoolTumor2-T 5 151347709 T TAC .
PoolTumor2-T 5 154505053 T TGTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA .
PoolTumor2-T 5 180046393 G GCCCCGACCCTGGCAGGTCCCCGTT .
PoolTumor2-T 5 180046495 AGG A .
PoolTumor2-T 5 180047629 TGAG T .
PoolTumor2-T 6 7516674 A ATATATACATATATATATATATATATG .
PoolTumor2-T 6 7518105 ATT A .
PoolTumor2-T 6 29760730 AC A .
PoolTumor2-T 6 31322200 G GCC .
PoolTumor2-T 6 54635601 TGGGCGG T .
PoolTumor2-T 6 67976248 C CGCTGTGCTGT .
PoolTumor2-T 6 104467207 CCTG C .
PoolTumor2-T 6 117686918 CA C .
PoolTumor2-T 6 155699472 TA T .
PoolTumor2-T 6 160640109 G GCAGCATCAGCAACAATAACAGCAACAATAGCAGCAGTAACAACAGCAA .
PoolTumor2-T 6 161781121 AT A .
PoolTumor2-T 6 162683814 TAAAAAA T .
PoolTumor2-T 7 1889435 T TGGCAGC .
PoolTumor2-T 7 6431523 C CT .
PoolTumor2-T 7 17751095 ATTTGT A .
PoolTumor2-T 7 18988889 CATT C .
PoolTumor2-T 7 33520405 TA T .
PoolTumor2-T 7 39403859 C CT .
PoolTumor2-T 7 43774485 CAG C .
PoolTumor2-T 7 45856989 T TAGG .
PoolTumor2-T 7 45864332 GTT G .
PoolTumor2-T 7 50444181 GT G .
PoolTumor2-T 7 55222610 G GAAA .
PoolTumor2-T 7 77519339 G GC .
PoolTumor2-T 7 106524644 CTG C .
PoolTumor2-T 7 140496901 TC T .
PoolTumor2-T 7 151948998 TA T .
PoolTumor2-T 7 152357777 A AT .
PoolTumor2-T 8 52001320 CA C .
PoolTumor2-T 8 116660509 T TG .
PoolTumor2-T 8 144351029 C CTGCTGCTGCTGCTGT .
PoolTumor2-T 8 144397798 G GGA .
PoolTumor2-T 8 144511953 ATGG A .
PoolTumor2-T 9 1159013 C CATTTATTT .
PoolTumor2-T 9 8331574 A AAACTTACCATTCTTGAACTGTAACT .
PoolTumor2-T 9 33676479 CA C .
PoolTumor2-T 9 36881930 T TG .
PoolTumor2-T 9 38354864 TCTG T .
PoolTumor2-T 9 101895040 CT C .
PoolTumor2-T 9 136206057 CAAGT C .
PoolTumor2-T 9 139162245 CA C .
PoolTumor2-T 9 139400835 T TAA .
PoolTumor2-T 9 139565475 TTGG T .
PoolTumor2-T 9 139565479 TGGG T .
PoolTumor2-T 10 33626149 T TCTCCACCGCTCCCCCCTGC .
PoolTumor2-T 10 36854110 C CTT .
PoolTumor2-T 10 39012451 AT A .
PoolTumor2-T 10 43572749 TTGC T .
PoolTumor2-T 10 88866085 TCA T .
PoolTumor2-T 10 89717709 AGCCGT A .
PoolTumor2-T 10 99804253 C CAGCAGCAGCAACAGCAGCAACAACAGCAGCAAT .
PoolTumor2-T 10 123240903 GACACACACACACAC G .
PoolTumor2-T 10 123241341 C CTTTTTTA .
PoolTumor2-T 11 17024874 CTGAGT C .
PoolTumor2-T 11 32450244 CG C .
PoolTumor2-T 11 86333429 TA T .
PoolTumor2-T 11 102199589 T TTA .
PoolTumor2-T 11 117226715 G GAGCAGCAGC .
PoolTumor2-T 12 9848470 A AGAT .
PoolTumor2-T 12 12013626 T TC .
PoolTumor2-T 12 12030236 C CTT .
PoolTumor2-T 12 25479744 T TTTA .
PoolTumor2-T 12 33759469 A ACAG .
PoolTumor2-T 12 40175197 C CT .
PoolTumor2-T 12 50480262 T TTGGTGG .
PoolTumor2-T 12 53085120 TCCGCCGCCATAGCCCCCACCGCTG T .
PoolTumor2-T 12 55215259 AGGT A .
PoolTumor2-T 12 72825422 GT G .
PoolTumor2-T 12 78288910 GA G .
PoolTumor2-T 12 82298589 G GC .
PoolTumor2-T 12 97487836 T TG .
PoolTumor2-T 12 97487836 T TTTG .
PoolTumor2-T 12 97487836 T TTTTG .
PoolTumor2-T 12 109203232 C CA .
PoolTumor2-T 12 121341076 A AC .
PoolTumor2-T 12 123810662 A AC .
PoolTumor2-T 12 124887058 G GGCTGCTGCTGCT .
PoolTumor2-T 13 28597449 CTT C .
PoolTumor2-T 13 28601389 TAC T .
PoolTumor2-T 13 28942716 T TATG .
PoolTumor2-T 13 43549921 AAC A .
PoolTumor2-T 13 72249648 ATT A .
PoolTumor2-T 14 19890157 GGCC G .
PoolTumor2-T 14 23652346 T TAAAA .
PoolTumor2-T 14 33960172 TGCA T .
PoolTumor2-T 14 36986190 A AC .
PoolTumor2-T 14 38910766 TAG T .
PoolTumor2-T 14 81574828 C CTTTTTTTTTCTTTTTT .
PoolTumor2-T 14 95315817 TC T .
PoolTumor2-T 14 95566068 TACACACACAC T .
PoolTumor2-T 14 95566068 TACACACACACACACAC T .
PoolTumor2-T 14 100660772 CT C .
PoolTumor2-T 15 38987651 T TCAGCAGCAGCAGCAG .
PoolTumor2-T 15 41991036 ATTTT A .
PoolTumor2-T 15 42049890 A AC .
PoolTumor2-T 15 59502492 TTGTACATTGAC T .
PoolTumor2-T 15 67457480 T TC .
PoolTumor2-T 15 67479678 A AG .
PoolTumor2-T 15 95828249 TG T .
PoolTumor2-T 16 5703497 T TTG .
PoolTumor2-T 16 9250812 C CT .
PoolTumor2-T 16 9553431 A AATG .
PoolTumor2-T 16 11476267 C CATTT .
PoolTumor2-T 16 15083569 C CGCA .
PoolTumor2-T 16 17380507 T TATCATCATCATCCTC .
PoolTumor2-T 16 56849811 G GTGC .
PoolTumor2-T 16 56866054 A AT .
PoolTumor2-T 16 56873613 T TA .
PoolTumor2-T 16 67645883 TGCAGTTACA T .
PoolTumor2-T 16 89846256 CT C .
PoolTumor2-T 17 29685481 CT C .
PoolTumor2-T 17 37880997 G GTGT .
PoolTumor2-T 17 39403721 A AGAAG .
PoolTumor2-T 17 41245586 C CT .
PoolTumor2-T 17 75649067 T TTGTG .
PoolTumor2-T 17 77386084 CAGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT C .
PoolTumor2-T 17 80200398 T TCTC .
PoolTumor2-T 18 13650245 T TTGC .
PoolTumor2-T 18 14153080 A AT .
PoolTumor2-T 18 39593388 CT C .
PoolTumor2-T 18 63927454 G GAAGA .
PoolTumor2-T 18 67646739 AGT A .
PoolTumor2-T 19 3270455 TG T .
PoolTumor2-T 19 7119636 G GACAC .
PoolTumor2-T 19 11144287 AT A .
PoolTumor2-T 19 13049895 TG T .
PoolTumor2-T 19 15311604 GC G .
PoolTumor2-T 19 19256768 TG T .
PoolTumor2-T 19 20828410 A AAAG .
PoolTumor2-T 19 28778494 A ATCATCGTCATCATCATCATCATCG .
PoolTumor2-T 19 30188521 TGGACACCC T .
PoolTumor2-T 19 30303714 TC T .
PoolTumor2-T 19 30311556 CCCT C .
PoolTumor2-T 19 33792731 G GGCGGGT .
PoolTumor2-T 19 41173904 TTGC T .
PoolTumor2-T 19 41727231 GGGTCAA G .
PoolTumor2-T 19 41749511 TC T .
PoolTumor2-T 19 52693297 C CT .
PoolTumor2-T 19 56089908 C CCCG .
PoolTumor2-T 20 26084383 GT G .
PoolTumor2-T 20 40407902 C CAGAT .
PoolTumor2-T 20 41306488 GA G .
PoolTumor2-T 20 44679205 C CT .
PoolTumor2-T 20 60476253 T TGAGCAG .
PoolTumor2-T 20 61024288 CACCG C .
PoolTumor2-T 21 10836460 G GGAATT .
PoolTumor2-T 21 11021018 TAA T .
PoolTumor2-T 21 11026527 C CAAAGAGGAAGGTAAGA .
PoolTumor2-T 21 15374334 TAA T .
PoolTumor2-T 21 38072579 A AT .
PoolTumor2-T 22 24118420 A AG .
PoolTumor2-T 22 24176677 GCAACAGGTCATGTTCAATTTCTT G .
PoolTumor2-T 22 30035219 AC A .
PoolTumor2-T 22 43788785 GGAGAGA G .
PoolTumor2-T X 1317593 TACACATACACAC T .
PoolTumor2-T X 47430509 A AGTGT .
PoolTumor2-T X 70341126 T TACTTTATCTGCTTC .
PoolTumor2-T X 72744762 C CT .
PoolTumor2-T X 100609517 G GA .
PoolTumor2-T X 122648760 C CAA .
PoolTumor2-T X 123202318 C CTATA .
PoolTumor2-T GL000229.1 8378 G GTCTC .
PoolTumor2-T GL000220.1 120127 CTTTCTTTCTT C .
PoolTumor2-T GL000220.1 121453 TTGCCTGCCTGCC T .
PoolTumor2-T GL000220.1 123842 TTTTCTTTC T .
PoolTumor2-T GL000220.1 128957 TTCTG T .
PoolTumor2-T GL000220.1 129282 T TTCTCTC .
PoolTumor2-T GL000220.1 132789 CCTCTCTCT C .
PoolTumor2-T GL000220.1 149811 C CG .
PoolTumor2-T GL000220.1 150715 G GC .
PoolTumor2-T GL000220.1 160369 CCT C .
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