From 66b88c0f5dfbdd39add657701dbec6382ae1c94f Mon Sep 17 00:00:00 2001 From: Ronak H Shah Date: Mon, 24 Jul 2017 13:50:16 -0400 Subject: [PATCH] Multiple Changes - For Pindel Modifying the output to remove the END tag in INFO - For Pindel default size of mutation has changed to 0 for 25 - For all make sure that there are two samples provided in the vcc - Adding the new sample output for PINDEL --- ...Tumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.txt | 250 ++++++++++++++++ ...Tumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf | 267 +++++++++++++++++- mutect/filter_mutect.py | 11 +- pindel/filter_pindel.py | 17 +- somaticindeldetector/filter_sid.py | 9 +- vardict/filter_vardict.py | 16 +- 6 files changed, 547 insertions(+), 23 deletions(-) diff --git a/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.txt b/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.txt index 81d1566..5730859 100644 --- a/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.txt +++ b/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.txt @@ -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 . diff --git a/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf b/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf index 58a20a1..04fb591 100644 --- a/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf +++ b/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf @@ -2,7 +2,6 @@ ##fileDate=20160822 ##source=pindel ##reference=hg19 -##INFO= ##INFO= ##INFO= ##INFO= @@ -15,11 +14,261 @@ ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PoolNormal-N PoolTumor2-T -2 6636086 . A AGCTTCGTTAAACTTCACTCGGAAGT . PASS END=6636086;HOMLEN=0;SVLEN=25;SVTYPE=INS GT:AD 0/0:554,1 0/0:719,10 -2 29451557 . GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G . PASS END=29451604;HOMLEN=7;HOMSEQ=AGGCAGG;SVLEN=-47;SVTYPE=DEL GT:AD 0/0:59,0 0/0:145,5 -5 154505053 . T TGTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA . PASS END=154505053;HOMLEN=0;SVLEN=40;SVTYPE=INS GT:AD 0/0:6,1 0/0:1,6 -6 7516674 . A ATATATACATATATATATATATATATG . PASS END=7516674;HOMLEN=6;HOMSEQ=TATATA;SVLEN=26;SVTYPE=INS GT:AD 0/0:23,0 0/1:22,11 -6 160640109 . G GCAGCATCAGCAACAATAACAGCAACAATAGCAGCAGTAACAACAGCAA . PASS END=160640109;HOMLEN=26;HOMSEQ=CAGCATCAGCAACAATAACAGCAACA;SVLEN=48;SVTYPE=INS GT:AD 0/0:108,0 0/0:96,8 -9 8331574 . A AAACTTACCATTCTTGAACTGTAACT . PASS END=8331574;HOMLEN=8;HOMSEQ=AACTTACC;SVLEN=25;SVTYPE=INS GT:AD 0/0:823,0 0/0:427,63 -10 99804253 . C CAGCAGCAGCAACAGCAGCAACAACAGCAGCAAT . PASS END=99804253;HOMLEN=32;HOMSEQ=AGCAGCAGCAACAGCAGCAACAACAGCAGCAA;SVLEN=33;SVTYPE=INS GT:AD 0/0:127,9 0/1:17,17 -17 77386084 . CAGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT C . PASS END=77386118;HOMLEN=21;HOMSEQ=AGCCTCCAGGTCTCCGCAGCC;SVLEN=-34;SVTYPE=DEL GT:AD 0/0:37,1 0/1:14,32 +1 658776 . GCAC G . PASS HOMLEN=4;HOMSEQ=CACC;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:59,0 0/0:74,8 +1 16200729 . A ATT . PASS HOMLEN=10;HOMSEQ=TTTTTTTTTT;SVLEN=2;SVTYPE=INS GT:AD 0/0:556,0 0/0:533,6 +1 16245610 . GT G . PASS HOMLEN=9;HOMSEQ=TTTTTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:182,6 0/1:158,61 +1 16975201 . CT C . PASS HOMLEN=0;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:5562,0 0/0:5722,332 +1 17085254 . GA G . PASS HOMLEN=0;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:990,0 0/0:1214,39 +1 17354373 . G GGAAGAA . PASS HOMLEN=24;HOMSEQ=GAAGAAGAAGAAGAAGAAGAAGAA;SVLEN=6;SVTYPE=INS GT:AD 0/0:360,0 0/0:313,39 +1 19043478 . C CG . PASS HOMLEN=0;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:2,6 +1 78414402 . GT G . PASS HOMLEN=6;HOMSEQ=TTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:591,1 0/0:455,6 +1 85733704 . TA T . PASS HOMLEN=6;HOMSEQ=AAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:394,0 0/0:418,6 +1 118161094 . GTC G . PASS HOMLEN=5;HOMSEQ=TCTCT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:641,15 0/0:640,141 +1 148643701 . AAAAC A . PASS HOMLEN=3;HOMSEQ=AAA;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:0,0 0/0:0,5 +1 148873257 . CT C . PASS HOMLEN=1;HOMSEQ=T;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:156,0 0/0:329,11 +1 150849071 . AC A . PASS HOMLEN=10;HOMSEQ=CCCCCCCCCC;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:5,0 0/1:6,5 +1 167509623 . T TAGC . PASS HOMLEN=37;HOMSEQ=AGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA;SVLEN=3;SVTYPE=INS GT:AD 0/0:7,0 0/0:3,5 +1 170778488 . CA C . PASS HOMLEN=4;HOMSEQ=AAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:0,0 0/1:3,7 +1 180810249 . GT G . PASS HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:286,0 0/0:451,5 +1 188263961 . AACAC A . PASS HOMLEN=24;HOMSEQ=ACACACACACACACACACACACAC;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:0,0 0/0:0,5 +1 193121496 . C CT . PASS HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:651,1 0/0:1009,11 +1 201189188 . C CT . PASS HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/1:5,5 +1 209812969 . TACACAC T . PASS HOMLEN=12;HOMSEQ=ACACACACACAC;SVLEN=-6;SVTYPE=DEL GT:AD 0/0:0,0 1/1:2,8 +1 229106423 . C CTG . PASS HOMLEN=2;HOMSEQ=TG;SVLEN=2;SVTYPE=INS GT:AD 0/0:26,1 0/1:41,16 +1 230331593 . G GT . PASS HOMLEN=3;HOMSEQ=TTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:2,6 +1 240683382 . A AAAAATAAAAT . PASS HOMLEN=36;HOMSEQ=AAAATAAAATAAAATAAAATAAAATAAAATAAAATA;SVLEN=10;SVTYPE=INS GT:AD 0/0:48,1 0/1:106,28 +2 6636086 . A AGCTTCGTTAAACTTCACTCGGAAGT . PASS HOMLEN=0;SVLEN=25;SVTYPE=INS GT:AD 0/0:554,1 0/0:719,10 +2 29451557 . GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G . PASS HOMLEN=7;HOMSEQ=AGGCAGG;SVLEN=-47;SVTYPE=DEL GT:AD 0/0:59,0 0/0:145,5 +2 29451675 . A AGGGCG . PASS HOMLEN=4;HOMSEQ=GGGC;SVLEN=5;SVTYPE=INS GT:AD 0/0:299,0 0/0:556,24 +2 44561591 . C CA . PASS HOMLEN=9;HOMSEQ=AAAAAAAAA;SVLEN=1;SVTYPE=INS GT:AD 0/0:223,1 0/0:207,5 +2 47096644 . ATTGT A . PASS HOMLEN=4;HOMSEQ=TTGT;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:10,0 0/1:3,8 +2 48033272 . ATTTTTGTTTTAATTCCT A . PASS HOMLEN=19;HOMSEQ=TTTTTGTTTTAATTCCTTT;SVLEN=-17;SVTYPE=DEL GT:AD 0/0:224,3 0/1:166,52 +2 48033546 . C CT . PASS HOMLEN=2;HOMSEQ=TT;SVLEN=1;SVTYPE=INS GT:AD 0/0:166,4 0/0:275,68 +2 48033846 . CAGTAAA C . PASS HOMLEN=2;HOMSEQ=AG;SVLEN=-6;SVTYPE=DEL GT:AD 0/0:181,0 0/1:174,84 +2 51288511 . T TACACACACACACACAC . PASS HOMLEN=43;HOMSEQ=ACACACACACACACACACACACACACACACACACACACACACA;SVLEN=16;SVTYPE=INS GT:AD 0/0:307,0 0/0:462,11 +2 51288525 . C CACACACACACACAT . PASS HOMLEN=13;HOMSEQ=ACACACACACACA;SVLEN=14;SVTYPE=INS GT:AD 0/0:347,1 0/0:483,14 +2 79423062 . TTTTG T . PASS HOMLEN=11;HOMSEQ=TTTGTTTGTTT;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:63,1 0/0:85,13 +2 91902876 . CAT C . PASS HOMLEN=2;HOMSEQ=AT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:182,0 0/0:287,31 +2 103352305 . G GCA . PASS HOMLEN=23;HOMSEQ=CACACACACACACACACACACAC;SVLEN=2;SVTYPE=INS GT:AD 0/0:0,0 0/0:2,6 +2 106021465 . ACT A . PASS HOMLEN=2;HOMSEQ=CT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:406,0 0/0:403,21 +2 111878556 . TGCCGCCGCCGCC T . PASS HOMLEN=30;HOMSEQ=GCCGCCGCCGCCGCCGCCGCCGCCGCCGCC;SVLEN=-12;SVTYPE=DEL GT:AD 0/0:4,0 0/1:3,7 +2 117248834 . T TG . PASS HOMLEN=2;HOMSEQ=GG;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:2,6 +2 134775262 . CAAA C . PASS HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:119,0 0/0:109,5 +2 144383034 . T TTGC . PASS HOMLEN=26;HOMSEQ=TGCTGCTGCTGCTGCTGCTGCTGCTG;SVLEN=3;SVTYPE=INS GT:AD 0/0:15,1 0/1:9,7 +2 204637705 . TTCATCATCATCA T . PASS HOMLEN=23;HOMSEQ=TCATCATCATCATCATCATCATC;SVLEN=-12;SVTYPE=DEL GT:AD 0/0:27,4 0/1:25,50 +2 209102117 . A ACT . PASS HOMLEN=1;HOMSEQ=C;SVLEN=2;SVTYPE=INS GT:AD 0/0:1,0 0/1:10,5 +2 209103969 . G GA . PASS HOMLEN=8;HOMSEQ=AAAAAAAA;SVLEN=1;SVTYPE=INS GT:AD 0/0:302,1 0/0:326,6 +2 236253185 . TCTCACACAGGCACA T . PASS HOMLEN=1;HOMSEQ=C;SVLEN=-14;SVTYPE=DEL GT:AD 0/0:2,0 0/0:0,6 +2 239604413 . TA T . PASS HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:0,0 0/0:2,6 +2 241405400 . C CGTG . PASS HOMLEN=1;HOMSEQ=G;SVLEN=3;SVTYPE=INS GT:AD 0/0:1,0 0/0:1,5 +3 37092173 . GTTC G . PASS HOMLEN=5;HOMSEQ=TTCTT;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:401,26 0/1:281,158 +3 47103861 . G GTT . PASS HOMLEN=14;HOMSEQ=TTTTTTTTTTTTTT;SVLEN=2;SVTYPE=INS GT:AD 0/0:341,1 0/0:295,5 +3 49725284 . CT C . PASS HOMLEN=0;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:1210,0 0/0:1191,77 +3 52620628 . GT G . PASS HOMLEN=3;HOMSEQ=TTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:689,0 0/0:495,5 +3 113802161 . CTGT C . PASS HOMLEN=33;HOMSEQ=TGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGT;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:14,0 0/0:24,5 +3 138423181 . CAT C . PASS HOMLEN=2;HOMSEQ=AT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:205,0 0/0:218,30 +3 142215120 . CTATATATATATATATA C . PASS HOMLEN=43;HOMSEQ=TATATATATATATATATATATATATATATATATATATATATAT;SVLEN=-16;SVTYPE=DEL GT:AD 0/0:23,0 0/1:20,16 +3 158104615 . CAAA C . PASS HOMLEN=11;HOMSEQ=AAAAAAAAAAA;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:78,1 0/0:80,8 +3 189507518 . C CAG . PASS HOMLEN=4;HOMSEQ=GGGG;SVLEN=2;SVTYPE=INS GT:AD 0/0:182,5 0/1:41,16 +3 194317814 . T TGCGTGCACACACCCACATGCACAC . PASS HOMLEN=26;HOMSEQ=GCGTGCACACACCCACATGCACACGC;SVLEN=24;SVTYPE=INS GT:AD 0/0:2,0 0/0:0,6 +3 195717078 . G GGCGCCAG . PASS HOMLEN=0;SVLEN=7;SVTYPE=INS GT:AD 0/0:353,0 0/0:383,7 +3 195717081 . C CGCGCCAG . PASS HOMLEN=0;SVLEN=7;SVTYPE=INS GT:AD 0/0:383,0 0/0:424,6 +3 197951869 . CGGT C . PASS HOMLEN=4;HOMSEQ=GGTG;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:57,0 0/0:75,6 +4 1809127 . CGTGT C . PASS HOMLEN=15;HOMSEQ=GTGTGTGTGTGTGTG;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:16,0 0/1:28,9 +4 8043638 . G GAA . PASS HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=2;SVTYPE=INS GT:AD 0/0:13,0 0/1:16,5 +4 38018679 . T TG . PASS HOMLEN=4;HOMSEQ=GGGG;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/1:3,7 +4 55953747 . CG C . PASS HOMLEN=4;HOMSEQ=GGGG;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:490,1 0/0:549,6 +4 55965031 . AT A . PASS HOMLEN=0;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:102,0 0/0:107,11 +4 66286113 . G GAA . PASS HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=2;SVTYPE=INS GT:AD 0/0:273,2 0/0:268,25 +4 66286113 . G GAAA . PASS HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=3;SVTYPE=INS GT:AD 0/0:273,0 0/0:268,7 +4 95616928 . C CT . PASS HOMLEN=11;HOMSEQ=TTTTTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:4,5 +4 116539618 . C CGA . PASS HOMLEN=16;HOMSEQ=GAGAGAGAGAGAGAGA;SVLEN=2;SVTYPE=INS GT:AD 0/0:0,0 0/0:2,6 +4 136777565 . CT C . PASS HOMLEN=3;HOMSEQ=TTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:102,0 0/1:85,26 +4 144106031 . T TC . PASS HOMLEN=2;HOMSEQ=CC;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:3,5 +5 14971859 . C CAA . PASS HOMLEN=8;HOMSEQ=AAAAAAAA;SVLEN=2;SVTYPE=INS GT:AD 0/0:0,0 0/0:2,6 +5 37744444 . GA G . PASS HOMLEN=3;HOMSEQ=AAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:0,0 0/1:8,5 +5 52074533 . C CTGT . PASS HOMLEN=8;HOMSEQ=TGTTGTTG;SVLEN=3;SVTYPE=INS GT:AD 0/0:88,3 0/1:52,20 +5 52665229 . GTCT AGAC . PASS HOMLEN=0;SVLEN=4;SVTYPE=INV;NTLEN=0,0 GT:AD 0/0:333,0 0/1:176,79 +5 57752811 . CA C . PASS HOMLEN=4;HOMSEQ=AAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:505,0 0/0:419,5 +5 57754489 . ACT A . PASS HOMLEN=2;HOMSEQ=CT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:312,8 0/1:322,144 +5 86669949 . A AAT . PASS HOMLEN=16;HOMSEQ=ATATATATATATATAT;SVLEN=2;SVTYPE=INS GT:AD 0/0:200,1 0/0:189,6 +5 112164716 . C CT . PASS HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:127,1 0/0:104,6 +5 112213678 . CTGTGTG C . PASS HOMLEN=35;HOMSEQ=TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT;SVLEN=-6;SVTYPE=DEL GT:AD 0/0:482,8 0/0:308,28 +5 112213678 . CTGTGTGTG C . PASS HOMLEN=33;HOMSEQ=TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT;SVLEN=-8;SVTYPE=DEL GT:AD 0/0:482,11 0/1:308,267 +5 149497110 . C CCA . PASS HOMLEN=0;SVLEN=2;SVTYPE=INS GT:AD 0/0:55,0 0/0:61,8 +5 151347709 . T TAC . PASS HOMLEN=12;HOMSEQ=ACACACACACAC;SVLEN=2;SVTYPE=INS GT:AD 0/0:2,0 0/0:3,5 +5 154505053 . T TGTGTGTGTGTGTGTGTGTGTATCACACACACACACATACA . PASS HOMLEN=0;SVLEN=40;SVTYPE=INS GT:AD 0/0:6,1 0/0:1,6 +5 180046393 . G GCCCCGACCCTGGCAGGTCCCCGTT . PASS HOMLEN=29;HOMSEQ=CCCCGACCCTGGCAGGTCCCCGTTCCCCG;SVLEN=24;SVTYPE=INS GT:AD 0/0:189,1 0/0:175,7 +5 180046495 . AGG A . PASS HOMLEN=3;HOMSEQ=GGG;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:388,1 0/0:520,29 +5 180047629 . TGAG T . PASS HOMLEN=11;HOMSEQ=GAGGAGGAGGA;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:650,1 0/0:801,10 +6 7516674 . A ATATATACATATATATATATATATATG . PASS HOMLEN=6;HOMSEQ=TATATA;SVLEN=26;SVTYPE=INS GT:AD 0/0:23,0 0/1:22,11 +6 7518105 . ATT A . PASS HOMLEN=11;HOMSEQ=TTTTTTTTTTT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:211,1 0/0:275,8 +6 29760730 . AC A . PASS HOMLEN=2;HOMSEQ=CC;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:455,0 0/0:422,86 +6 31322200 . G GCC . PASS HOMLEN=4;HOMSEQ=CCCC;SVLEN=2;SVTYPE=INS GT:AD 0/0:21,0 0/1:12,6 +6 54635601 . TGGGCGG T . PASS HOMLEN=3;HOMSEQ=GGG;SVLEN=-6;SVTYPE=DEL GT:AD 0/0:46,1 0/0:41,6 +6 67976248 . C CGCTGTGCTGT . PASS HOMLEN=20;HOMSEQ=GCTGTGCTGTGCTGTGCTGT;SVLEN=10;SVTYPE=INS GT:AD 0/0:0,0 0/0:1,5 +6 104467207 . CCTG C . PASS HOMLEN=33;HOMSEQ=CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:8,0 0/1:4,7 +6 117686918 . CA C . PASS HOMLEN=7;HOMSEQ=AAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:387,1 0/0:539,12 +6 155699472 . TA T . PASS HOMLEN=8;HOMSEQ=AAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:67,0 0/0:80,6 +6 160640109 . G GCAGCATCAGCAACAATAACAGCAACAATAGCAGCAGTAACAACAGCAA . PASS HOMLEN=26;HOMSEQ=CAGCATCAGCAACAATAACAGCAACA;SVLEN=48;SVTYPE=INS GT:AD 0/0:108,0 0/0:96,8 +6 161781121 . AT A . PASS HOMLEN=6;HOMSEQ=TTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:823,1 0/0:771,10 +6 162683814 . TAAAAAA T . PASS HOMLEN=15;HOMSEQ=AAAAAAAAAAAAAAA;SVLEN=-6;SVTYPE=DEL GT:AD 0/0:114,1 0/0:120,6 +7 1889435 . T TGGCAGC . PASS HOMLEN=14;HOMSEQ=GGCAGCGGCAGCGG;SVLEN=6;SVTYPE=INS GT:AD 0/0:0,0 0/0:2,5 +7 6431523 . C CT . PASS HOMLEN=1;HOMSEQ=T;SVLEN=1;SVTYPE=INS GT:AD 0/0:446,0 0/0:674,21 +7 17751095 . ATTTGT A . PASS HOMLEN=32;HOMSEQ=TTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTT;SVLEN=-5;SVTYPE=DEL GT:AD 0/0:0,0 0/0:0,6 +7 18988889 . CATT C . PASS HOMLEN=2;HOMSEQ=AT;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:17,0 0/0:26,6 +7 33520405 . TA T . PASS HOMLEN=0;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:0,0 0/0:2,6 +7 39403859 . C CT . PASS HOMLEN=15;HOMSEQ=TTTTTTTTTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:2,6 +7 43774485 . CAG C . PASS HOMLEN=11;HOMSEQ=AGAGAGAGAGA;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:18,0 0/1:20,5 +7 45856989 . T TAGG . PASS HOMLEN=0;SVLEN=3;SVTYPE=INS GT:AD 0/0:26,1 0/1:19,16 +7 45864332 . GTT G . PASS HOMLEN=10;HOMSEQ=TTTTTTTTTT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:0,0 0/0:3,6 +7 50444181 . GT G . PASS HOMLEN=9;HOMSEQ=TTTTTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:164,1 0/0:273,9 +7 55222610 . G GAAA . PASS HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=3;SVTYPE=INS GT:AD 0/0:263,0 0/0:586,8 +7 77519339 . G GC . PASS HOMLEN=9;HOMSEQ=CCCCCCCCC;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/1:4,6 +7 106524644 . CTG C . PASS HOMLEN=4;HOMSEQ=TGTG;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:569,0 0/0:640,58 +7 140496901 . TC T . PASS HOMLEN=2;HOMSEQ=CC;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:819,0 0/1:854,291 +7 151948998 . TA T . PASS HOMLEN=8;HOMSEQ=AAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:330,1 0/0:340,7 +7 152357777 . A AT . PASS HOMLEN=6;HOMSEQ=TTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:782,0 0/0:689,43 +8 52001320 . CA C . PASS HOMLEN=15;HOMSEQ=AAAAAAAAAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:0,0 0/0:2,6 +8 116660509 . T TG . PASS HOMLEN=2;HOMSEQ=GG;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/1:7,5 +8 144351029 . C CTGCTGCTGCTGCTGT . PASS HOMLEN=2;HOMSEQ=TG;SVLEN=15;SVTYPE=INS GT:AD 0/0:0,0 0/1:5,5 +8 144397798 . G GGA . PASS HOMLEN=4;HOMSEQ=GAGA;SVLEN=2;SVTYPE=INS GT:AD 0/0:0,0 0/0:3,5 +8 144511953 . ATGG A . PASS HOMLEN=27;HOMSEQ=TGGTGGTGGTGGTGGTGGTGGTGGTGG;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:0,0 0/0:2,7 +9 1159013 . C CATTTATTT . PASS HOMLEN=36;HOMSEQ=ATTTATTTATTTATTTATTTATTTATTTATTTATTT;SVLEN=8;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,6 +9 8331574 . A AAACTTACCATTCTTGAACTGTAACT . PASS HOMLEN=8;HOMSEQ=AACTTACC;SVLEN=25;SVTYPE=INS GT:AD 0/0:823,0 0/0:427,63 +9 33676479 . CA C . PASS HOMLEN=4;HOMSEQ=AAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:435,1 0/0:418,5 +9 36881930 . T TG . PASS HOMLEN=8;HOMSEQ=GGGGGGGG;SVLEN=1;SVTYPE=INS GT:AD 0/0:129,0 0/0:190,6 +9 38354864 . TCTG T . PASS HOMLEN=44;HOMSEQ=CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:6,0 0/0:1,5 +9 101895040 . CT C . PASS HOMLEN=4;HOMSEQ=TTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:464,0 0/0:381,7 +9 136206057 . CAAGT C . PASS HOMLEN=3;HOMSEQ=AAG;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:11,0 0/1:8,10 +9 139162245 . CA C . PASS HOMLEN=0;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:2,0 0/1:7,5 +9 139400835 . T TAA . PASS HOMLEN=14;HOMSEQ=AAAAAAAAAAAAAA;SVLEN=2;SVTYPE=INS GT:AD 0/0:13,0 0/1:18,6 +9 139565475 . TTGG T . PASS HOMLEN=3;HOMSEQ=TGG;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:376,1 0/0:228,13 +9 139565479 . TGGG T . PASS HOMLEN=12;HOMSEQ=GGGGGGGGGGGG;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:305,22 0/1:182,115 +10 33626149 . T TCTCCACCGCTCCCCCCTGC . PASS HOMLEN=2;HOMSEQ=CT;SVLEN=19;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,6 +10 36854110 . C CTT . PASS HOMLEN=16;HOMSEQ=TTTTTTTTTTTTTTTT;SVLEN=2;SVTYPE=INS GT:AD 0/0:89,2 0/1:44,13 +10 39012451 . AT A . PASS HOMLEN=1;HOMSEQ=T;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:52,0 0/1:36,21 +10 43572749 . TTGC T . PASS HOMLEN=12;HOMSEQ=TGCTGCTGCTGC;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:363,1 0/0:516,8 +10 88866085 . TCA T . PASS HOMLEN=2;HOMSEQ=CA;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:230,0 0/0:129,15 +10 89717709 . AGCCGT A . PASS HOMLEN=0;SVLEN=-5;SVTYPE=DEL GT:AD 0/0:715,0 0/1:309,192 +10 99804253 . C CAGCAGCAGCAACAGCAGCAACAACAGCAGCAAT . PASS HOMLEN=32;HOMSEQ=AGCAGCAGCAACAGCAGCAACAACAGCAGCAA;SVLEN=33;SVTYPE=INS GT:AD 0/0:127,9 0/1:17,17 +10 123240903 . GACACACACACACAC G . PASS HOMLEN=19;HOMSEQ=ACACACACACACACACACA;SVLEN=-14;SVTYPE=DEL GT:AD 0/0:213,5 0/0:136,24 +10 123241341 . C CTTTTTTA . PASS HOMLEN=12;HOMSEQ=TTTTTTATTTTT;SVLEN=7;SVTYPE=INS GT:AD 0/0:665,20 0/1:150,85 +11 17024874 . CTGAGT C . PASS HOMLEN=6;HOMSEQ=TGAGTT;SVLEN=-5;SVTYPE=DEL GT:AD 0/0:11,0 0/0:1,6 +11 32450244 . CG C . PASS HOMLEN=7;HOMSEQ=GGGGGGG;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:56,0 0/1:90,44 +11 86333429 . TA T . PASS HOMLEN=11;HOMSEQ=AAAAAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:298,11 0/1:272,90 +11 102199589 . T TTA . PASS HOMLEN=23;HOMSEQ=TATATATATATATATATATATAT;SVLEN=2;SVTYPE=INS GT:AD 0/0:64,1 0/0:122,16 +11 117226715 . G GAGCAGCAGC . PASS HOMLEN=8;HOMSEQ=AGCAGCAG;SVLEN=9;SVTYPE=INS GT:AD 0/0:50,2 0/1:15,6 +12 9848470 . A AGAT . PASS HOMLEN=20;HOMSEQ=GATGATGATGATGATGATGA;SVLEN=3;SVTYPE=INS GT:AD 0/0:152,3 0/0:127,14 +12 12013626 . T TC . PASS HOMLEN=7;HOMSEQ=CCCCCCC;SVLEN=1;SVTYPE=INS GT:AD 0/0:1761,3 0/0:1647,347 +12 12030236 . C CTT . PASS HOMLEN=16;HOMSEQ=TTTTTTTTTTTTTTTT;SVLEN=2;SVTYPE=INS GT:AD 0/0:224,1 0/0:203,6 +12 25479744 . T TTTA . PASS HOMLEN=4;HOMSEQ=TTAT;SVLEN=3;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,6 +12 33759469 . A ACAG . PASS HOMLEN=20;HOMSEQ=CAGCAGCAGCAGCAGCAGCA;SVLEN=3;SVTYPE=INS GT:AD 0/0:7,1 0/0:2,5 +12 40175197 . C CT . PASS HOMLEN=0;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/1:7,9 +12 50480262 . T TTGGTGG . PASS HOMLEN=22;HOMSEQ=TGGTGGTGGTGGTGGTGGTGGT;SVLEN=6;SVTYPE=INS GT:AD 0/0:35,2 0/1:37,17 +12 53085120 . TCCGCCGCCATAGCCCCCACCGCTG T . PASS HOMLEN=8;HOMSEQ=CCGCCGCC;SVLEN=-24;SVTYPE=DEL GT:AD 0/0:3,0 0/1:8,5 +12 55215259 . AGGT A . PASS HOMLEN=10;HOMSEQ=GGTGGTGGTG;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:440,1 0/0:429,5 +12 72825422 . GT G . PASS HOMLEN=12;HOMSEQ=TTTTTTTTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:8,0 0/1:17,9 +12 78288910 . GA G . PASS HOMLEN=9;HOMSEQ=AAAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:69,0 0/0:80,5 +12 82298589 . G GC . PASS HOMLEN=1;HOMSEQ=C;SVLEN=1;SVTYPE=INS GT:AD 0/0:61,0 0/0:50,11 +12 97487836 . T TG . PASS HOMLEN=0;SVLEN=1;SVTYPE=INS GT:AD 0/0:272,1 0/0:168,6 +12 97487836 . T TTTG . PASS HOMLEN=2;HOMSEQ=TT;SVLEN=3;SVTYPE=INS GT:AD 0/0:272,0 0/0:168,12 +12 97487836 . T TTTTG . PASS HOMLEN=3;HOMSEQ=TTT;SVLEN=4;SVTYPE=INS GT:AD 0/0:272,6 0/0:168,23 +12 109203232 . C CA . PASS HOMLEN=15;HOMSEQ=AAAAAAAAAAAAAAA;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:3,5 +12 121341076 . A AC . PASS HOMLEN=5;HOMSEQ=CCCCC;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:3,5 +12 123810662 . A AC . PASS HOMLEN=5;HOMSEQ=CCCCC;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,8 +12 124887058 . G GGCTGCTGCTGCT . PASS HOMLEN=37;HOMSEQ=GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG;SVLEN=12;SVTYPE=INS GT:AD 0/0:10,0 0/1:23,8 +13 28597449 . CTT C . PASS HOMLEN=6;HOMSEQ=TTTTTT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:320,3 0/0:238,19 +13 28601389 . TAC T . PASS HOMLEN=1;HOMSEQ=A;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:381,0 0/1:275,87 +13 28942716 . T TATG . PASS HOMLEN=19;HOMSEQ=ATGATGATGATGATGATGA;SVLEN=3;SVTYPE=INS GT:AD 0/0:494,0 0/0:445,7 +13 43549921 . AAC A . PASS HOMLEN=13;HOMSEQ=ACACACACACACA;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:275,1 0/0:249,7 +13 72249648 . ATT A . PASS HOMLEN=9;HOMSEQ=TTTTTTTTT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:257,2 0/0:260,24 +14 19890157 . GGCC G . PASS HOMLEN=3;HOMSEQ=GCC;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:1,0 0/1:13,6 +14 23652346 . T TAAAA . PASS HOMLEN=21;HOMSEQ=AAAAAAAAAAAAAAAAAAAAA;SVLEN=4;SVTYPE=INS GT:AD 0/0:211,1 0/0:281,8 +14 33960172 . TGCA T . PASS HOMLEN=18;HOMSEQ=GCAGCAGCAGCAGCAGCA;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:27,0 0/0:46,7 +14 36986190 . A AC . PASS HOMLEN=4;HOMSEQ=CCCC;SVLEN=1;SVTYPE=INS GT:AD 0/0:2,0 0/1:50,26 +14 38910766 . TAG T . PASS HOMLEN=2;HOMSEQ=AG;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:2,0 0/1:18,14 +14 81574828 . C CTTTTTTTTTCTTTTTT . PASS HOMLEN=9;HOMSEQ=TTTTTTTTT;SVLEN=16;SVTYPE=INS GT:AD 0/0:388,1 0/0:324,6 +14 95315817 . TC T . PASS HOMLEN=7;HOMSEQ=CCCCCCC;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:0,0 0/0:2,6 +14 95566068 . TACACACACAC T . PASS HOMLEN=31;HOMSEQ=ACACACACACACACACACACACACACACACA;SVLEN=-10;SVTYPE=DEL GT:AD 0/0:60,2 0/0:46,10 +14 95566068 . TACACACACACACACAC T . PASS HOMLEN=25;HOMSEQ=ACACACACACACACACACACACACA;SVLEN=-16;SVTYPE=DEL GT:AD 0/0:77,2 0/0:60,13 +14 100660772 . CT C . PASS HOMLEN=1;HOMSEQ=T;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:0,0 0/0:2,6 +15 38987651 . T TCAGCAGCAGCAGCAG . PASS HOMLEN=36;HOMSEQ=CAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG;SVLEN=15;SVTYPE=INS GT:AD 0/0:5,0 0/0:0,6 +15 41991036 . ATTTT A . PASS HOMLEN=11;HOMSEQ=TTTTTTTTTTT;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:297,0 0/0:297,6 +15 42049890 . A AC . PASS HOMLEN=1;HOMSEQ=C;SVLEN=1;SVTYPE=INS GT:AD 0/0:218,0 0/0:241,45 +15 59502492 . TTGTACATTGAC T . PASS HOMLEN=0;SVLEN=-11;SVTYPE=DEL GT:AD 0/0:438,0 0/1:209,97 +15 67457480 . T TC . PASS HOMLEN=4;HOMSEQ=CCCC;SVLEN=1;SVTYPE=INS GT:AD 0/0:198,0 0/1:349,231 +15 67479678 . A AG . PASS HOMLEN=1;HOMSEQ=G;SVLEN=1;SVTYPE=INS GT:AD 0/0:701,0 0/0:778,122 +15 95828249 . TG T . PASS HOMLEN=5;HOMSEQ=GGGGG;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:0,0 0/0:2,6 +16 5703497 . T TTG . PASS HOMLEN=2;HOMSEQ=TG;SVLEN=2;SVTYPE=INS GT:AD 0/0:0,0 0/0:3,5 +16 9250812 . C CT . PASS HOMLEN=13;HOMSEQ=TTTTTTTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:5,0 0/1:15,6 +16 9553431 . A AATG . PASS HOMLEN=26;HOMSEQ=ATGATGATGATGATGATGATGATGAT;SVLEN=3;SVTYPE=INS GT:AD 0/0:0,0 0/0:1,5 +16 11476267 . C CATTT . PASS HOMLEN=5;HOMSEQ=ATTTA;SVLEN=4;SVTYPE=INS GT:AD 0/0:0,0 0/0:1,6 +16 15083569 . C CGCA . PASS HOMLEN=8;HOMSEQ=GCAGCAGC;SVLEN=3;SVTYPE=INS GT:AD 0/0:2,0 0/0:0,7 +16 17380507 . T TATCATCATCATCCTC . PASS HOMLEN=39;HOMSEQ=ATCATCATCATCCTCATCATCATCATCCTCATCATCATC;SVLEN=15;SVTYPE=INS GT:AD 0/0:10,1 0/1:11,12 +16 56849811 . G GTGC . PASS HOMLEN=17;HOMSEQ=TGCTGCTGCTGCTGCTG;SVLEN=3;SVTYPE=INS GT:AD 0/0:4,0 0/0:4,5 +16 56866054 . A AT . PASS HOMLEN=6;HOMSEQ=TTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:131,1 0/0:217,44 +16 56873613 . T TA . PASS HOMLEN=1;HOMSEQ=A;SVLEN=1;SVTYPE=INS GT:AD 0/0:181,5 0/0:227,41 +16 67645883 . TGCAGTTACA T . PASS HOMLEN=0;SVLEN=-9;SVTYPE=DEL GT:AD 0/0:709,0 0/1:389,115 +16 89846256 . CT C . PASS HOMLEN=3;HOMSEQ=TTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:502,0 0/0:457,5 +17 29685481 . CT C . PASS HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:282,1 0/0:321,7 +17 37880997 . G GTGT . PASS HOMLEN=0;SVLEN=3;SVTYPE=INS GT:AD 0/0:1102,0 0/1:804,541 +17 39403721 . A AGAAG . PASS HOMLEN=18;HOMSEQ=GAAGGAAGGAAGGAAGGA;SVLEN=4;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,5 +17 41245586 . C CT . PASS HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:885,1 0/0:980,15 +17 75649067 . T TTGTG . PASS HOMLEN=23;HOMSEQ=TGTGTGTGTGTGTGTGTGTGTGT;SVLEN=4;SVTYPE=INS GT:AD 0/0:1,0 0/0:0,5 +17 77386084 . CAGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT C . PASS HOMLEN=21;HOMSEQ=AGCCTCCAGGTCTCCGCAGCC;SVLEN=-34;SVTYPE=DEL GT:AD 0/0:37,1 0/1:14,32 +17 80200398 . T TCTC . PASS HOMLEN=5;HOMSEQ=CTCCT;SVLEN=3;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,6 +18 13650245 . T TTGC . PASS HOMLEN=25;HOMSEQ=TGCTGCTGCTGCTGCTGCTGCTGCT;SVLEN=3;SVTYPE=INS GT:AD 0/0:8,1 0/0:2,5 +18 14153080 . A AT . PASS HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:366,0 0/0:463,5 +18 39593388 . CT C . PASS HOMLEN=7;HOMSEQ=TTTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:254,0 0/0:218,6 +18 63927454 . G GAAGA . PASS HOMLEN=8;HOMSEQ=AAGAAAGA;SVLEN=4;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,5 +18 67646739 . AGT A . PASS HOMLEN=11;HOMSEQ=GTGTGTGTGTG;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:0,0 0/1:4,6 +19 3270455 . TG T . PASS HOMLEN=3;HOMSEQ=GGG;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:1,0 0/0:2,6 +19 7119636 . G GACAC . PASS HOMLEN=14;HOMSEQ=ACACACACACACAC;SVLEN=4;SVTYPE=INS GT:AD 0/0:259,1 0/0:252,7 +19 11144287 . AT A . PASS HOMLEN=7;HOMSEQ=TTTTTTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:94,0 0/0:139,5 +19 13049895 . TG T . PASS HOMLEN=7;HOMSEQ=GGGGGGG;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:462,2 0/0:472,11 +19 15311604 . GC G . PASS HOMLEN=4;HOMSEQ=CCCC;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:172,0 0/0:222,6 +19 19256768 . TG T . PASS HOMLEN=6;HOMSEQ=GGGGGG;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:386,0 0/0:388,5 +19 20828410 . A AAAG . PASS HOMLEN=0;SVLEN=3;SVTYPE=INS GT:AD 0/0:2,0 0/0:0,6 +19 28778494 . A ATCATCGTCATCATCATCATCATCG . PASS HOMLEN=9;HOMSEQ=TCATCGTCA;SVLEN=24;SVTYPE=INS GT:AD 0/0:2,0 0/0:3,5 +19 30188521 . TGGACACCC T . PASS HOMLEN=8;HOMSEQ=GGACACCC;SVLEN=-8;SVTYPE=DEL GT:AD 0/0:0,0 0/0:0,5 +19 30303714 . TC T . PASS HOMLEN=6;HOMSEQ=CCCCCC;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:406,0 0/0:517,6 +19 30311556 . CCCT C . PASS HOMLEN=2;HOMSEQ=CC;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:146,0 0/0:210,8 +19 33792731 . G GGCGGGT . PASS HOMLEN=21;HOMSEQ=GCGGGTGCGGGTGCGGGTGCG;SVLEN=6;SVTYPE=INS GT:AD 0/0:225,3 0/0:236,24 +19 41173904 . TTGC T . PASS HOMLEN=17;HOMSEQ=TGCTGCTGCTGCTGCTG;SVLEN=-3;SVTYPE=DEL GT:AD 0/0:38,0 0/0:91,6 +19 41727231 . GGGTCAA G . PASS HOMLEN=6;HOMSEQ=GGTCAA;SVLEN=-6;SVTYPE=DEL GT:AD 0/0:111,0 0/1:135,35 +19 41749511 . TC T . PASS HOMLEN=6;HOMSEQ=CCCCCC;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:1086,2 0/0:1296,17 +19 52693297 . C CT . PASS HOMLEN=0;SVLEN=1;SVTYPE=INS GT:AD 0/0:150,0 0/0:192,43 +19 56089908 . C CCCG . PASS HOMLEN=2;HOMSEQ=CC;SVLEN=3;SVTYPE=INS GT:AD 0/0:0,0 0/0:1,5 +20 26084383 . GT G . PASS HOMLEN=3;HOMSEQ=TTT;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:105,0 0/0:131,10 +20 40407902 . C CAGAT . PASS HOMLEN=4;HOMSEQ=AGAT;SVLEN=4;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,6 +20 41306488 . GA G . PASS HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:248,4 0/0:372,80 +20 44679205 . C CT . PASS HOMLEN=0;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/1:4,6 +20 60476253 . T TGAGCAG . PASS HOMLEN=21;HOMSEQ=GAGCAGGAGCAGGAGCAGGAG;SVLEN=6;SVTYPE=INS GT:AD 0/0:2,0 0/0:1,5 +20 61024288 . CACCG C . PASS HOMLEN=4;HOMSEQ=ACCG;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:0,0 0/0:0,7 +21 10836460 . G GGAATT . PASS HOMLEN=2;HOMSEQ=GA;SVLEN=5;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,6 +21 11021018 . TAA T . PASS HOMLEN=1;HOMSEQ=A;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:884,15 0/0:933,104 +21 11026527 . C CAAAGAGGAAGGTAAGA . PASS HOMLEN=22;HOMSEQ=AAAGAGGAAGGTAAGAAAAGAG;SVLEN=16;SVTYPE=INS GT:AD 0/0:50,2 0/1:49,21 +21 15374334 . TAA T . PASS HOMLEN=9;HOMSEQ=AAAAAAAAA;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:308,1 0/0:362,7 +21 38072579 . A AT . PASS HOMLEN=7;HOMSEQ=TTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/0:3,5 +22 24118420 . A AG . PASS HOMLEN=1;HOMSEQ=G;SVLEN=1;SVTYPE=INS GT:AD 0/0:0,0 0/1:6,5 +22 24176677 . GCAACAGGTCATGTTCAATTTCTT G . PASS HOMLEN=26;HOMSEQ=CAACAGGTCATGTTCAATTTCTTCAA;SVLEN=-23;SVTYPE=DEL GT:AD 0/0:566,24 0/1:446,142 +22 30035219 . AC A . PASS HOMLEN=5;HOMSEQ=CCCCC;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:536,1 0/0:677,7 +22 43788785 . GGAGAGA G . PASS HOMLEN=18;HOMSEQ=GAGAGAGAGAGAGAGAGA;SVLEN=-6;SVTYPE=DEL GT:AD 0/0:14,0 0/1:9,5 +X 1317593 . TACACATACACAC T . PASS HOMLEN=5;HOMSEQ=ACACA;SVLEN=-12;SVTYPE=DEL GT:AD 0/0:267,2 0/0:171,22 +X 47430509 . A AGTGT . PASS HOMLEN=32;HOMSEQ=GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT;SVLEN=4;SVTYPE=INS GT:AD 0/0:76,1 0/1:60,21 +X 70341126 . T TACTTTATCTGCTTC . PASS HOMLEN=0;SVLEN=14;SVTYPE=INS GT:AD 0/0:219,0 0/0:162,5 +X 72744762 . C CT . PASS HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=1;SVTYPE=INS GT:AD 0/0:152,0 0/0:147,5 +X 100609517 . G GA . PASS HOMLEN=8;HOMSEQ=AAAAAAAA;SVLEN=1;SVTYPE=INS GT:AD 0/0:181,0 0/0:184,7 +X 122648760 . C CAA . PASS HOMLEN=15;HOMSEQ=AAAAAAAAAAAAAAA;SVLEN=2;SVTYPE=INS GT:AD 0/0:188,0 0/0:221,5 +X 123202318 . C CTATA . PASS HOMLEN=3;HOMSEQ=TAT;SVLEN=4;SVTYPE=INS GT:AD 0/0:70,0 0/0:100,11 +GL000229.1 8378 . G GTCTC . PASS HOMLEN=13;HOMSEQ=TCTCTCTCTCTCT;SVLEN=4;SVTYPE=INS GT:AD 0/0:0,0 0/0:0,5 +GL000220.1 120127 . CTTTCTTTCTT C . PASS HOMLEN=1;HOMSEQ=T;SVLEN=-10;SVTYPE=DEL GT:AD 0/0:49,0 0/0:42,5 +GL000220.1 121453 . TTGCCTGCCTGCC T . PASS HOMLEN=37;HOMSEQ=TGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCT;SVLEN=-12;SVTYPE=DEL GT:AD 0/0:12,0 0/1:11,5 +GL000220.1 123842 . TTTTCTTTC T . PASS HOMLEN=27;HOMSEQ=TTTCTTTCTTTCTTTCTTTCTTTCTTT;SVLEN=-8;SVTYPE=DEL GT:AD 0/0:52,0 0/0:43,5 +GL000220.1 128957 . TTCTG T . PASS HOMLEN=7;HOMSEQ=TCTGTCT;SVLEN=-4;SVTYPE=DEL GT:AD 0/0:98,0 0/0:106,7 +GL000220.1 129282 . T TTCTCTC . PASS HOMLEN=30;HOMSEQ=TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC;SVLEN=6;SVTYPE=INS GT:AD 0/0:65,0 0/0:61,6 +GL000220.1 132789 . CCTCTCTCT C . PASS HOMLEN=30;HOMSEQ=CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT;SVLEN=-8;SVTYPE=DEL GT:AD 0/0:61,1 0/0:56,7 +GL000220.1 149811 . C CG . PASS HOMLEN=6;HOMSEQ=GGGGGG;SVLEN=1;SVTYPE=INS GT:AD 0/0:31,0 0/0:50,7 +GL000220.1 150715 . G GC . PASS HOMLEN=5;HOMSEQ=CCCCC;SVLEN=1;SVTYPE=INS GT:AD 0/0:39,0 0/0:50,8 +GL000220.1 160369 . CCT C . PASS HOMLEN=15;HOMSEQ=CTCTCTCTCTCTCTC;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:19,2 0/1:9,10 diff --git a/mutect/filter_mutect.py b/mutect/filter_mutect.py index d6b3767..aba06fb 100644 --- a/mutect/filter_mutect.py +++ b/mutect/filter_mutect.py @@ -68,14 +68,19 @@ def RunStdFilter(args): else: vcf_out = vcf_out + "_STDfilter.vcf" txt_out = txt_out + "_STDfilter.txt" - vcf_reader = vcf.Reader(open(args.inputVcf, 'r')) + vcf_reader = vcf.Reader(open(args.inputVcf, 'r')) vcf_reader.infos['FAILURE_REASON'] = VcfInfo('FAILURE_REASON', '1', 'String', 'Failure Reason from MuTect text File') vcf_writer = vcf.Writer(open(vcf_out, 'w'), vcf_reader) txtDF = pd.read_table(args.inputTxt, skiprows=1, low_memory=False) txt_fh = open(txt_out, "wb") allsamples = vcf_reader.samples - sample1 = allsamples[0] - sample2 = allsamples[1] + if(len(allsamples) == 2): + sample1 = allsamples[0] + sample2 = allsamples[1] + else: + if(args.verbose): + logger.critical("The VCF does not have two sample columns.Please input a proper vcf with Tumor/Normal columns") + sys.exit(1) if(sample1 == args.tsampleName): nsampleName = sample2 else: diff --git a/pindel/filter_pindel.py b/pindel/filter_pindel.py index a5daa52..381d546 100644 --- a/pindel/filter_pindel.py +++ b/pindel/filter_pindel.py @@ -115,9 +115,9 @@ def main(): action="store", dest="min", required=False, - default=25, + default=0, type=int, - metavar='25', + metavar='0', help="Minimum length of the indels") parser.add_argument( "-max", @@ -158,12 +158,18 @@ def RunStdFilter(args): vcf_out = vcf_out + "_STDfilter.vcf" txt_out = txt_out + "_STDfilter.txt" vcf_reader = vcf.Reader(open(args.inputVcf, 'r')) + del vcf_reader.infos['END'] vcf_reader.formats['DP'] = VcfFormat('DP', '1', 'Integer', 'Total coverage at the site') vcf_writer = vcf.Writer(open(vcf_out, 'w'), vcf_reader) txt_fh = open(txt_out, "wb") allsamples = vcf_reader.samples - sample1 = allsamples[0] - sample2 = allsamples[1] + if(len(allsamples) == 2): + sample1 = allsamples[0] + sample2 = allsamples[1] + else: + if(args.verbose): + logger.critical("The VCF does not have two sample columns.Please input a proper vcf with Tumor/Normal columns") + sys.exit(1) if(sample1 == args.tsampleName): nsampleName = sample2 else: @@ -172,6 +178,7 @@ def RunStdFilter(args): tcall = record.genotype(args.tsampleName) recordType = record.INFO['SVTYPE'] recordLen = abs(int(record.INFO['SVLEN'])) + record.INFO.pop('END',0) # print tcall, "recordType: ",recordType, "recordLen: ", recordLen if(tcall['AD'] is not None): @@ -198,8 +205,8 @@ def RunStdFilter(args): else: nvf = 0 # print "Ndata: ",trd,tad - nvfRF = int(args.tnr) * nvf + # print recordLen, args.min, args.max if(args.hotspotVcf): hotspotFlag = checkHotspot(args.hotspotVcf, record.CHROM, record.POS) diff --git a/somaticindeldetector/filter_sid.py b/somaticindeldetector/filter_sid.py index afbaed9..a7a6e0e 100644 --- a/somaticindeldetector/filter_sid.py +++ b/somaticindeldetector/filter_sid.py @@ -149,8 +149,13 @@ def RunStdFilter(args): vcf_writer = vcf.Writer(open(vcf_out, 'w'), vcf_reader) txt_fh = open(txt_out, "wb") allsamples = vcf_reader.samples - sample1 = allsamples[0] - sample2 = allsamples[1] + if(len(allsamples) == 2): + sample1 = allsamples[0] + sample2 = allsamples[1] + else: + if(args.verbose): + logger.critical("The VCF does not have two sample columns.Please input a proper vcf with Tumor/Normal columns") + sys.exit(1) if(sample1 == args.tsampleName): nsampleName = sample2 else: diff --git a/vardict/filter_vardict.py b/vardict/filter_vardict.py index 7564537..b35e816 100644 --- a/vardict/filter_vardict.py +++ b/vardict/filter_vardict.py @@ -140,8 +140,13 @@ def RunStdFilter(args): vcf_writer = vcf.Writer(open(vcf_out, 'w'), vcf_reader) txt_fh = open(txt_out, "wb") allsamples = vcf_reader.samples - sample1 = allsamples[0] - sample2 = allsamples[1] + if(len(allsamples) == 2): + sample1 = allsamples[0] + sample2 = allsamples[1] + else: + if(args.verbose): + logger.critical("The VCF does not have two sample columns.Please input a proper vcf with Tumor/Normal columns") + sys.exit(1) if(sample1 == args.tsampleName): nsampleName = sample2 else: @@ -175,9 +180,12 @@ def RunStdFilter(args): nvf = nad / ndp else: nvf = 0 - # print "Ndata: ",trd,tad - nvfRF = int(args.tnr) * nvf + else: + logger.critical("filter_vardict: There are no genotype values for Normal. We will exit.") + sys.exit(1) + # print "Ndata: ",trd,tad + if(args.hotspotVcf): hotspotFlag = checkHotspot(args.hotspotVcf, record.CHROM, record.POS) else: