From 43df2725a98ec6c2b5f4b313f5ce8688bbe23e23 Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Fri, 22 Mar 2024 14:21:49 +0100 Subject: [PATCH 1/5] Add annotate delly test files --- .../mtuberculosis/annotated_delly.vcf | 98 ++++++++++++++++++ .../converged_who_fohm_tbdb.bed.gz | Bin 0 -> 1230 bytes .../converged_who_fohm_tbdb.bed.gz.tbi | Bin 0 -> 535 bytes tests/fixtures/mtuberculosis/delly.bcf | Bin 0 -> 8153 bytes 4 files changed, 98 insertions(+) create mode 100644 tests/fixtures/mtuberculosis/annotated_delly.vcf create mode 100644 tests/fixtures/mtuberculosis/converged_who_fohm_tbdb.bed.gz create mode 100644 tests/fixtures/mtuberculosis/converged_who_fohm_tbdb.bed.gz.tbi create mode 100644 tests/fixtures/mtuberculosis/delly.bcf diff --git a/tests/fixtures/mtuberculosis/annotated_delly.vcf b/tests/fixtures/mtuberculosis/annotated_delly.vcf new file mode 100644 index 0000000..6413816 --- /dev/null +++ b/tests/fixtures/mtuberculosis/annotated_delly.vcf @@ -0,0 +1,98 @@ +##fileformat=VCFv4.2 +##FILTER= +##fileDate=20240320 +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##reference=/fs1/pipelines/jasen/assets/tbdb/converged_who_fohm_tbdb.fasta +##contig= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tb_test_1 +Chromosome 79571 DEL00000000 C 4432 PASS IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=83034;PE=81;MAPQ=60;CT=3to5;CIPOS=-116,116;CIEND=-116,116 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-448.606,-24.0894,0:10000:PASS:1263:0:1163:0:0:81:0:0 +Chromosome 335663 DEL00000001 CCCGCCCGTGAGGGCTACTACGCCGCCGCCGGCGCCGCCGGCG C 170 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=335705;PE=0;MAPQ=0;CT=3to5;CIPOS=-18,18;CIEND=-18,18;SRMAPQ=60;INSLEN=0;HOMLEN=23;SR=3;SRQ=0.986667;CONSENSUS=GCCCCCGCCGACTCCGGCGGCGCCGAAGAGCAGGCCGGCGTTGCCGCCAGCCCCGCCGGCGCCGCCGGCCCCGCCGGCGCCGAACAGCATGGCGTTGCCGCCGGCTCCGCCGGACCCGCCGCTCCCACTGCTGGCGACCCCGCCAGCGCC;CE=1.60897;CONSBP=70 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-35.9948,-3.60715,0:36:PASS:430:150:473:0:0:0:0:12 +Chromosome 336122 DEL00000002 C 1711 PASS IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=338558;PE=32;MAPQ=60;CT=3to5;CIPOS=-50,50;CIEND=-50,50 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-240.796,-13.5426,0:135:PASS:195:121:567:0:0:45:0:0 +Chromosome 336681 DEL00000003 G 47 LowQual IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=1188981;PE=4;MAPQ=12;CT=3to5;CIPOS=-589,589;CIEND=-589,589;gene=fgd1,mshA,ccsA,rpoB,rpoC,mmpL5,mmpS5,mmpR5,rpsL,rplC;locus_tag=Rv0407,Rv0486,Rv0529,Rv0667,Rv0668,Rv0676c,Rv0677c,Rv0678,Rv0682,Rv0701 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-1.08764,0,-44.5085:11:LowQual:225618:555892:286157:2:8:4:0:0 +Chromosome 426942 DEL00000004 AGCCGATGTTGTTGTTGCCGGTGTTGGCAATGCCCTGGTTGAAGTTGCCCGCGTTGGCCATGCCAAAGTTGTTGTCGCCCAGGTTGAACAGGCCCATGTTGGCGATGCCGGCGTTCAGCGGGCCGAACCCGATCTGGTTGTCGCCGGACAGGCCGAT A 929 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=427098;PE=0;MAPQ=0;CT=3to5;CIPOS=-27,27;CIEND=-27,27;SRMAPQ=60;INSLEN=0;HOMLEN=27;SR=16;SRQ=0.990244;CONSENSUS=AAACCGTTGTTGCCGGCGCCGGAGTTCAGGGAGCTGAAGCCGGACAAGCCGTCGCCGGTCAGCCCGATGCCGACGTTGTTGTTGCCGGTGTTGAACAAGCCGATGTTGTTGTTGCCGGTGTTGCCGAAGCCGATGTTGTAGTTACCGGTGTTGCCGACACCGATGTTGTAGTTGCCGGTGTTGCCGATACCGATGTTGTTGAAAG;CE=1.9542;CONSBP=98 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-112.37,-11.409,0:114:PASS:5185:1075:4689:0:0:0:0:38 +Chromosome 576459 DEL00000005 CCGCGGCGGTGGGCGGGCTGCCCGTCGCGGTG C 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=576490;PE=0;MAPQ=0;CT=3to5;CIPOS=-8,8;CIEND=-8,8;SRMAPQ=60;INSLEN=0;HOMLEN=8;SR=2;SRQ=0.981982;CONSENSUS=TGCCGACCTACTCCGAGTCGTTCGGCCTGGTGGCTGTGGAGGCCCAAGCGTGCGGCACACCGGTGGTGGCCGCGACGGGATCACCGGCACCCTGGTGTCCGGGCACGAGGT;CE=1.85921;CONSBP=70;gene=mshA;locus_tag=Rv0486 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-8.44223,-179.974:84:PASS:2444:3623:1431:2:0:0:64:4 +Chromosome 673144 DEL00000006 C 180 PASS IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=674133;PE=3;MAPQ=60;CT=3to5;CIPOS=-267,267;CIEND=-267,267 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-6.86191,0,-192.862:69:PASS:13888:35590:33759:1:34:3:0:0 +Chromosome 745879 DEL00000007 GGGCGCACCTGCAGGCCGACATCGCGTTGAGCATTCCCGCCGGCGCGCCGC G 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=745929;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=60;INSLEN=0;HOMLEN=8;SR=2;SRQ=1;CONSENSUS=GTGCTGGGCGGCGTGGTCGACGTCGTGTGTCCGCTCGGCTGGCCGGCCACACCGGCTCGGTTGCCGTTCACGCTGGGCGCCGGCGGGACCGTATCCGGTCCGCGCGCAGCTGCGCGTCGTCGACACGGCGGTACCGGCCG;CE=1.75836;CONSBP=83 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-27.3734,-344.95:10000:PASS:4094:8730:4464:2:0:0:118:3 +Chromosome 888992 DEL00000008 AACCTCAACACCCCCTCAAGTGAAGGAGG A 1195 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=889020;PE=0;MAPQ=0;CT=3to5;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=60;INSLEN=0;HOMLEN=0;SR=20;SRQ=1;CONSENSUS=CTCTTGGGGTTGGCGTTGAGCAGTATTGCCGGCACTAGGTGAGAAGGACCGGCCGGCGTGACTTGATAGGAGCGTGGCTTTCGCCCCGACTGAGATGTGTCCGCCGACCGGCCCATGAACCGCCCCGGCATGTCCGGAGACTCCAGTTCTTGGAAAGGATGGGGTCATGTCAGGTG;CE=1.94461;CONSBP=115 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-464.773,0,-134.821:10000:PASS:4558:4609:1682:1:0:0:70:180 +Chromosome 889021 DEL00000009 T 118 LowQual IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3711934;PE=15;MAPQ=8;CT=3to5;CIPOS=-261,261;CIEND=-261,261;gene=fbiC,Rv1258c,embR,atpE,rrs,rrl,fabG1,inhA,rpsA,tlyA,ndh,katG,PPE35,Rv1979c,pncA,kasA,eis,ahpC,folC,pepQ,ribD,Rv2752c,thyX,thyA,ald,fbiD,Rv3083,fprA,whiB7,Rv3236c,fbiA,fbiB;locus_tag=Rv1173,Rv1258c,Rv1267c,Rv1305,EBG00000313325,EBG00000313339,Rv1483,Rv1484,Rv1630,Rv1694,Rv1854c,Rv1908c,Rv1918c,Rv1979c,Rv2043c,Rv2245,Rv2416c,Rv2428,Rv2447c,Rv2535c,Rv2671,Rv2752c,Rv2754c,Rv2764c,Rv2780,Rv2983,Rv3083,Rv3106,Rv3197A,Rv3236c,Rv3261,Rv3262 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-17.9337,-273.799:10000:PASS:586595:1839942:445619:4:84:15:0:0 +Chromosome 1086194 DEL00000010 GATCATCCCGCCTTCCTCGTAGTCCTTGCCCACCATGTAGCCGGTGGTGTTGTGTAAGAACAACAGCGGCGTGTCGGCCCGGTTGGCCAGCTGGATGAACTGGGTGGCCTTCTGTGATTCCTCGCTGAACAGCACGCCGCGGGCGTTGGCCAGGATGCCCAGCGGATAGCCGTGCAACCGAGCCCAGCCGGTCACCAGAGACGACCCGTACAGCGGCTTGAATTCGTCGAACTCGGAGC G 1200 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=1086432;PE=0;MAPQ=0;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=20;SRQ=1;CONSENSUS=ATGCCGTAGTGCCCGGCGCCGTAGGACGCGCCGATCAGCAGCGAGATGTGCGGGACGGTCGAGTTGGACACGGCGTTGATCATCATCGAGCCATGCTTGCATCGACGATGCGGGCGATCACCTCGCGCGGGTCGAATGGGATGCGCAGATCCGGGGGCACGATGCCGA;CE=1.91853;CONSBP=99 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-614.911,-61.6221,0:10000:PASS:24952:149:22617:0:0:0:0:205 +Chromosome 1389302 DEL00000011 GAGCCGAACGCCTCGTCGCTGTTTGATGTCTCCTCGAGCGTTCGGCTGAGCGAACTC G 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=1389358;PE=0;MAPQ=0;CT=3to5;CIPOS=-18,18;CIEND=-18,18;SRMAPQ=60;INSLEN=0;HOMLEN=18;SR=2;SRQ=1;CONSENSUS=TGGCTAAACCCTGTACGCCGAGCATCGGCTTACCGAGCCGAACGCCTCGTCGAGGATCTCCTGCTGTTCGACGGCGTGCACCTTCGACGAGCCTGACGACGGGGCTGACATCGCCCGGCG;CE=1.92435;CONSBP=35 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-13.8466,-209.97:138:PASS:4421:7853:3228:2:0:0:73:3 +Chromosome 1541946 DEL00000012 C 6350 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=1543304;PE=86;MAPQ=60;CT=3to5;CIPOS=-6,6;CIEND=-6,6;SRMAPQ=60;INSLEN=0;HOMLEN=5;SR=20;SRQ=1;CONSENSUS=CCTGGCCGGTCCGGTACTCGTCCGCGGGCGGAGGCCGCCTTCGAAGAAATCCTTTGAGAATTCGCCAAGGCCGTCGACCCAGCATGGGGTCAGCTCGCCAGCCGCGCCGGCTGGCAACCGTTCCCGCTCGAGAAAGACCTGGAGGAATACCAGTGACAAACGACCTCCCAGAC;CE=1.92567;CONSBP=98 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-338.951,-33.9673,0:10000:PASS:478:0:478:0:0:86:0:113 +Chromosome 1633539 DEL00000013 G 632 PASS IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=1636881;PE=11;MAPQ=60;CT=3to5;CIPOS=-216,216;CIEND=-216,216 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-57.7815,0,-36.5816:10000:PASS:352:1034:571:2:7:11:0:0 +Chromosome 1741362 DEL00000014 CCGCGCGCCGGCGACCCGGGTAGACACCGCGATCACCACCGGATCGCTCCCGTCTCGACAGTGGCGACGGACTCCCTCGATCACGGCGGCCCCGGCATTGCCCGAGCCCAGCGCCTCCAGCACCACGGCG C 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=1741491;PE=0;MAPQ=0;CT=3to5;CIPOS=-13,13;CIEND=-13,13;SRMAPQ=60;INSLEN=0;HOMLEN=13;SR=2;SRQ=0.991935;CONSENSUS=CGCGGTACCATCACCGCGCCAGCCTCCACCAGGTCGTGCCCGGGACCATAGCTTGCGCCGACCCGCGCGCCGGCTGCCACACAGGCGTCCATCGCCACCGCGTCACTTCCCGGATAGACGGCGA;CE=1.83056;CONSBP=63 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-22.2632,-293.957:10000:PASS:10196:20810:9239:2:0:0:101:3 +Chromosome 1752599 DEL00000015 G 114 LowQual IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3528674;PE=8;MAPQ=15;CT=3to5;CIPOS=-525,525;CIEND=-525,525;gene=rpsA,tlyA,ndh,katG,PPE35,Rv1979c,pncA,kasA,eis,ahpC,folC,pepQ,ribD,Rv2752c,thyX,thyA,ald,fbiD,Rv3083,fprA;locus_tag=Rv1630,Rv1694,Rv1854c,Rv1908c,Rv1918c,Rv1979c,Rv2043c,Rv2245,Rv2416c,Rv2428,Rv2447c,Rv2535c,Rv2671,Rv2752c,Rv2754c,Rv2764c,Rv2780,Rv2983,Rv3083,Rv3106 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-2.44736,-216.756:24:PASS:588906:1146813:567367:2:38:8:0:0 +Chromosome 1983916 DEL00000016 C 36 LowQual IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2638985;PE=6;MAPQ=6;CT=3to5;CIPOS=-498,498;CIEND=-498,498;gene=ndh,katG,PPE35,Rv1979c,pncA,kasA;locus_tag=Rv1854c,Rv1908c,Rv1918c,Rv1979c,Rv2043c,Rv2245 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-4.82883,-129.154:48:PASS:212940:414765:212900:2:22:6:0:0 +Chromosome 2108603 DEL00000017 CCGCCGGCGCCGGCACCGGCTCCTGCAGAGCCCGCTCCGG C 240 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2108642;PE=0;MAPQ=0;CT=3to5;CIPOS=-14,14;CIEND=-14,14;SRMAPQ=60;INSLEN=0;HOMLEN=16;SR=4;SRQ=1;CONSENSUS=GTATGGCTCGGGACCGCCAACAACCCGGTGGACAAGGGCGCGGCCAAGGCGCTGGCCGAATCGATCCGGCCTTTGGTCGCCCCGCCGCCGGCGCCGGCCGGGGAAGTCGCTCCTACCCCGACGACACCGACACCGCAGCGGACCTTACCGGCCTGA;CE=1.83735;CONSBP=85 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-12.2797,0,-57.2732:123:PASS:1611:2076:1801:1:0:0:22:7 +Chromosome 2345119 DEL00000018 ACGGTCAGCGATCGCGTGCCAGGGCTGTCGGCGGCGATGGATGCGGTGATCGCCACTGCGATGGCCAAGGATCCCATGCGTCGGTTCACCTCAGCGGGTGAATTCGCACATGCCGCCGCCG A 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2345239;PE=0;MAPQ=0;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SRMAPQ=60;INSLEN=0;HOMLEN=11;SR=2;SRQ=0.978571;CONSENSUS=GCTACTAACCGGTGAGGCGCCGTTTGCCGCCGGTGCTGGAGCGGCGGTGGCAGTGGTGGCGAGTCACCTGCACCAACCGCCGCCGACAGCCCTGTACGGGGGAGCCACCGACGGATGGGTGCCGCCGAGCCCCGCGCCGC;CE=1.82104;CONSBP=86 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-21.6557,-263.962:10000:PASS:9258:18068:7295:2:0:0:90:2 +Chromosome 2365410 DEL00000019 G 4980 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2366768;PE=63;MAPQ=60;CT=3to5;CIPOS=-6,6;CIEND=-6,6;SRMAPQ=60;INSLEN=0;HOMLEN=6;SR=20;SRQ=1;CONSENSUS=CACTTCGGCACGGACACGGCTCGTTCGACGGACGTCGTGACCAGAAGTCGAGCAAACCGACTCCACTCTAGCTAGTGATACAAGCTTTTTTGTAGCCGCGCGATTGGGCCGCCCGTAAGGAATGCGTCATGAGCGACTTCGCATCACGGGCGACCAATCATTAATTTGTCAAA;CE=1.99254;CONSBP=100 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-449.935,-45.0893,0:10000:PASS:377:14:376:0:9:63:0:150 +Chromosome 2375746 DEL00000020 TCGTCGGCGTGGCCGACGACCAGAGCCCGATGAC T 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2375779;PE=0;MAPQ=0;CT=3to5;CIPOS=-8,8;CIEND=-8,8;SRMAPQ=60;INSLEN=0;HOMLEN=8;SR=2;SRQ=1;CONSENSUS=GAGGCCGTCTGGCAGGTCCTCGGCGATCAGGGGATCAGCCAGCCAAACAACGCGTTCCTCGTCGGCCAGGATCTCGCGCAAGGTGGATATCTCGCCGACCGCCTCGAA;CE=1.93251;CONSBP=59 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-12.657,-245.964:127:PASS:2495:4777:2353:2:0:0:87:5 +Chromosome 2381150 DEL00000021 TGCTGGCCGCGGCCAGGGCGTGGCACGC T 118 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2381177;PE=0;MAPQ=0;CT=3to5;CIPOS=-11,11;CIEND=-11,11;SRMAPQ=60;INSLEN=0;HOMLEN=13;SR=2;SRQ=1;CONSENSUS=TGGCTGTCCACCGGCATGGGCCCCGGTCCGCTGCTGGCCGCGCAATACACCGAAATTGCAACGGAACTCGCAAGCGTGCTCGCTGCGG;CE=1.91293;CONSBP=32 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-21.0736,-329.952:10000:PASS:2608:5244:2498:2:0:0:115:5 +Chromosome 2387320 DEL00000022 CCGCCGCCGGCCCCGCCCTCGCCGCCGCTGCCCATGGCGCCGTGGGCGCCCGAGTGGCCACTGAGCCAGCCGCCCGCCCCGCCCGCGCCACCGGCACCGCGGGCACCTCCGG C 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2387431;PE=0;MAPQ=0;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SRMAPQ=60;INSLEN=0;HOMLEN=12;SR=2;SRQ=1;CONSENSUS=TGCCGGGATTCGTGCCTGTCGACGTACCACCGCCGGCACCAGCCTCGCCGCGCGCACCGCCGCCGCCGCCGGTGCCACCATCGCCACCATCGCCGCCGTCACCGCCGCGGCCACCGAA;CE=1.73136;CONSBP=63 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-4.48976,0,-31.4859:45:PASS:2641:1851:398:1:0:0:12:3 +Chromosome 2430113 DEL00000023 T 4188 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2431471;PE=50;MAPQ=60;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=60;INSLEN=0;HOMLEN=4;SR=20;SRQ=1;CONSENSUS=GGGCAAATGGGTGGCAAGTGGGGCCAAGTGGGGCACAACTGGGGCTCAAACCGGACTCAATATCGCCGACAGCCGGTGACGACCCGGCTGGGGCTTCCCGAGACTGCGATTCCCAAACGATGACGCCCAAACAAAAAGCGGGACCGCCGATGGCTGCCCCGCTGCCGCTGGTTGCGTTCGGCTTACTA;CE=1.9381;CONSBP=89 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-170.374,-17.1326,0:10000:PASS:327:0:421:0:0:50:0:57 +Chromosome 2535431 DEL00000024 C 3180 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2536141;PE=33;MAPQ=60;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=20;SRQ=1;CONSENSUS=GGGTTGCCAGCACAAATCCGCCCATACCCGTCCACGCCCGCAGCGCGCCCTCCCACGACGTCGGCGCGGCCCGCACCACTAACAGCAGTGGGACCAAGCAGGTCGTACGCCCCGATGACGGCCTATGGCCAGTCGAAGCTGGCGGTCTTGATGTTCGCCCGCGAGCTGGACCGCCGCAGCCGCGCGGC;CE=1.85796;CONSBP=99 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-461.933,-46.2917,0:10000:PASS:64980:116:70079:0:0:34:0:154 +Chromosome 2550008 DEL00000025 C 6120 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2551366;PE=82;MAPQ=60;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=60;INSLEN=0;HOMLEN=6;SR=20;SRQ=1;CONSENSUS=CGATGCGCGACAATCATCGGGTCGTCAGTCTGGCCCAGCGGCAAAGCATCCGCCACACCGCAAGTCCCTCCCAAGGCGATCACCAGCGCCACCGCGCCCAACATAGCCGTCTTCACCATCGGTCCCCTTCAGGCTTTCCCCACCGTAGAAACGTGCGCAATGCGCGGCGCA;CE=1.90112;CONSBP=89 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-479.93,-48.0953,0:10000:PASS:402:51:369:0:0:82:0:160 +Chromosome 2635551 DEL00000026 A 180 PASS IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2638985;PE=3;MAPQ=60;CT=3to5;CIPOS=-430,430;CIEND=-430,430 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-14.9897,0,-38.9897:150:PASS:500:680:921:1:7:3:0:0 +Chromosome 2729618 DEL00000027 CGGCCTCGTCGAGGTGTAGCCCTTCCCGACGCGCGGCGTACCAGACCCAGCGCAGAAACGTTGCCTGCGTTGGGCCTTCGTCGGCCGGTGATGTCAGCCTGACCGTCGTTCGATACTCGGCGGCTCCTCGGGCAATTGTGGCGGGCACGACCCCGGGCTTAACATGCGGTAGCGCGCTGGCAGCCCTGTTCAGCATGGCGCATACCTTGTCCGGG C 1200 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2729832;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=2;SR=20;SRQ=0.99422;CONSENSUS=AGCCAGCGACTGCTGATCGCTAGAGCTCAGTCGCAGCTCGGGCCCCACCACCGTGCGCAGGGCGGACTCCACACGTTCGGCCGTCGAGAACTCGTCGTCGGATCGGACGTGGAAAATGTGGTCGTGATCGAGCATTCGTGCGCCCCGGCCGGCCGGCTGAGATTGGTAAAAGC;CE=1.93516;CONSBP=99 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-506.927,-50.8006,0:10000:PASS:20976:302:14539:0:0:0:0:169 +Chromosome 2784611 DEL00000028 T 5670 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2785969;PE=75;MAPQ=60;CT=3to5;CIPOS=-6,6;CIEND=-6,6;SRMAPQ=60;INSLEN=0;HOMLEN=5;SR=20;SRQ=1;CONSENSUS=CGGCGCGAATTGCTGGCCACCCGGAACTTGACGACCTCTTGATCACCGACTTTGCGGCGCTGCAAATCGTTGACGATGTGACCGACCACGGTCAGTGGCGTTTCGAACATTTGCTCATTCCTTTCCTAGTTGCGTTGGCACAGTTGCGTTGGCACCGGGTGATTCCGCGAACTGCCCACGCATATGC;CE=1.97451;CONSBP=92 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-395.943,-39.6786,0:10000:PASS:419:45:380:0:0:75:0:132 +Chromosome 2839459 DEL00000029 ACGCGCTCAACCAGCTCGCGAGCAGACGCAGAGTCGCATGAAAATCCGGATTTCGATGCGATTCTGCGTCTGCT A 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2839532;PE=0;MAPQ=0;CT=3to5;CIPOS=-9,9;CIEND=-9,9;SRMAPQ=60;INSLEN=0;HOMLEN=8;SR=2;SRQ=0.992908;CONSENSUS=GCTCCTCGAGATCACACCGCACCGACGGCAACACCTCACGGACGCGCTCACGGGGCCTCCAGGATGGCGACCGCGGCCGCGGTATCCCCTTCGTGGGTCAGCGACAAATGGATCGTCACGTCGGCCAAATACTCAGCGATG;CE=1.91775;CONSBP=42 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-8.36556,0,-116.35:84:PASS:5269:5231:5375:1:0:0:44:8 +Chromosome 2863437 DEL00000030 TGGCCAGCGCGCGCGGCACCGTGGAGATCGGCTTCATC T 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2863474;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=2;SR=2;SRQ=0.992424;CONSENSUS=CACGACCCCGGCCGCCGGCACCGCGCACACATCCGAGCGCTGATGGATGGCGACGGCCTCATCGCCGGTCGCCAGGTCGACGGTGCCGCGCGCACCCGCAGCGGCTGCCCGTTGGTCATCCCGCCTTCCAGC;CE=1.79864;CONSBP=84 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-22.2632,-293.957:10000:PASS:2637:5293:2730:2:0:0:101:3 +Chromosome 2972105 DEL00000031 T 4476 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=2973463;PE=55;MAPQ=60;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=60;INSLEN=0;HOMLEN=5;SR=20;SRQ=1;CONSENSUS=TTTAAACGGTTGGAGCGGCTGACCGCCGGTGCCCGGGATGGGCCCCGGCGGCAACTTGTCCAACGGGCGACGCTCACGTCCACGCTTGCGCAGCTCATCTTCGGCGGCCTTGCGTGCCTGCTCAGCCTGGCGGCGCCAAGCCTCATAGCGACGCCGAATCTCCCTCTCAATCGCGCGCTGCACACCCATCCGGAAC;CE=1.90327;CONSBP=100 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-287.958,-28.8572,0:10000:PASS:399:35:355:0:0:57:0:96 +Chromosome 3007066 DEL00000032 CGCCGCTCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCGGGTCACTGGCGCCGCTCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCGGGTCACTGGCGCCGCTCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCGGGTCAATCGAAGAT C 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3007229;PE=0;MAPQ=0;CT=3to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=60;INSLEN=0;HOMLEN=4;SR=2;SRQ=1;CONSENSUS=CTACCGCCGTTCGCGGGCGCTCCGGTGACCAACGTCAGATTCACTGCATCGTCGCCGGCGCGGGTCACTGGCGCCCCGTCACGTGTCACCGGGAGCCGCGTGCGGCTGTAACGTCTTGATCCGCTCCGACGACGTCAGTTGCCAAGGC;CE=1.89425;CONSBP=72 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-313.249,0,-57.0261:10000:PASS:14198:10628:15323:1:0:0:35:126 +Chromosome 3007119 DEL00000033 CGCCGCTCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCGGGTCACTGGCGCCGCTCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCGGGTCAATCGAAGAT C 117 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3007229;PE=0;MAPQ=0;CT=3to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=45;INSLEN=0;HOMLEN=4;SR=4;SRQ=1;CONSENSUS=CATCGTCGCCGGCGCGGGTCACTGGCGCCGCTCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCGGGTCACTGGCGCCCCGTCACGTGTCACCGGGAGCCGCGTGCGGCTGTAACGTCTTGATCCGCTCCGACGACGTCAGTTGCCAAG;CE=1.85634;CONSBP=79 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-331.205,-9.14062,0:91:PASS:4985:5898:9720:1:0:0:11:128 +Chromosome 3037359 DEL00000034 CCGGGGCGCGCCAGCCGCTGCGAGCGTAACGCCACGGCGAGCTTGCGTGCACCGAATTCGCCGTGGCGTTACGCT C 180 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3037433;PE=0;MAPQ=0;CT=3to5;CIPOS=-9,9;CIEND=-9,9;SRMAPQ=60;INSLEN=0;HOMLEN=9;SR=3;SRQ=0.993289;CONSENSUS=TGGTGGCACTGCCCATGGATGCCCTCCGGGGAAGAAAATTCTGGTGCCCAACAATACCAACCGGGCGGTTGGTCGGCAGGTAGCCGCGGCGCGAACTCGCGCAAGGTGGCAGCCAGCGCCTCCGGGACACGGGCCTTGATCCGGGTGCC;CE=1.90954;CONSBP=84 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-0.582023,0,-66.5725:7:LowQual:3996:3502:3193:1:0:0:25:3 +Chromosome 3551226 DEL00000035 T 3240 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3552584;PE=34;MAPQ=60;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=20;SRQ=0.994118;CONSENSUS=TATCCTTAGCTATGCGCATGTTCCCAAAAGTGTTCCCGCCCATGAAAACGGCCCCCGGAGTCTCCTCCGAGGGCCATTTCGCCGGTAGCGGGGACAGGATTCGAACCTGCGACCTCTGGGTTATGAGCTAACCAGTCGCAATCTCTCCCATCGCGGTCGGTCTCATACGT;CE=1.97469;CONSBP=101 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-422.538,-42.3833,0:10000:PASS:526:0:57:0:0:34:0:141 +Chromosome 3551231 DEL00000036 G 2040 PASS IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3554067;PE=34;MAPQ=60;CT=3to5;CIPOS=-289,289;CIEND=-289,289 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-204,-10.235,0:102:PASS:1041:57:1131:0:0:34:0:0 +Chromosome 3552709 DEL00000037 G 4166 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3554067;PE=50;MAPQ=60;CT=3to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=60;INSLEN=0;HOMLEN=4;SR=20;SRQ=1;CONSENSUS=AACCAGTCGCAATCTCTCCCATCGCGGTCGGTCTCATACGTCCAGATCAGCCTCTATTCCGCCGTCCAGCCTGTTCCGCCGCGTCGCGGTTGTACGGATTCGTTTCGGCCTGTTCTGTTCCCAAATCCGTTCCCAACACAGCAATCAGCAGCAATCCCAGGCCGAAATCGGTCAGACTCTTGGTGGAC;CE=1.9585;CONSBP=97 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-446.935,-44.7887,0:10000:PASS:57:0:500:0:0:50:0:149 +Chromosome 3663727 DEL00000038 ACCTGTGAGTCGAGTGAGCGGAACGAACGAAGTGAGTGACGGGAACGAGACGAACAATCCGGCAGAAGTGAGTGACGGGAACGAGACGAACAATCCGGCAGAAGTGAGTGACGGGAACGAGACGAACAATCCGGCC A 73 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3663862;PE=0;MAPQ=0;CT=3to5;CIPOS=-63,63;CIEND=-63,63;SRMAPQ=27;INSLEN=0;HOMLEN=62;SR=3;SRQ=1;CONSENSUS=GCCCAAAAAGCATGGGAACGTGCCCCTGTGAGTCGAGTGAGCGGAACGAACCTGTGAGTCGAGTGAGCGGAACGAACGAAGTGAGTGACGGGAACGAGACGAACAATCCGGCCCCTGTGAGTCGAGTGAGCGGAACGAACGAAGTGAGTG;CE=1.90282;CONSBP=50 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-57.5329,-3.5551,0:36:PASS:11752:3121:1973:0:0:0:1:21 +Chromosome 3737291 DEL00000039 T 120 LowQual IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3738292;PE=2;MAPQ=60;CT=3to5;CIPOS=-501,501;CIEND=-501,501 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-7.16293,0,-187.163:72:PASS:193:220:101:1:33:3:0:0 +Chromosome 3737445 DEL00000040 AGCCGCCCTTGCCGCCGAAAAAGCCGCTGCCGCCGGCGCCGCCGGCGCCGCCGCCACCGCCGCTGCCGCCTTGGGTGACGGAGCTGTTGCCGCCGACGCCGTCACCGCCGTGGCCACCGTCGCCGCCCTTGCCGCCCTCGCCGGAGCTAAGGCTGCCGTTTCCGCCGGCGCCGCCAGCGCCACCGGCCCCACCGGAACCGCCGACGATGCCGCTGTTGGCGCCGATCGAGCCCCCGTTGCCGCCGGCACCGCCGTTGCCGCCCTTGCCGCCGTCGCCACCTGAGCCGTTGGGGTTGCTGCCACCGGC A 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3737751;PE=0;MAPQ=0;CT=3to5;CIPOS=-17,17;CIEND=-17,17;SRMAPQ=60;INSLEN=0;HOMLEN=16;SR=2;SRQ=1;CONSENSUS=CCGCCGTTGGGGCCGCCCTGACCGCCGTCGCCGCCGAAGCCGCCCTTGCCGCCGTTGCCGCCGGGGGCGCCCGTGACCCCGATGGAGGCGGGGCCGCTGGTAGCGCCGAAGCTCCCATCACCGCCATTGCCACCGGCGCCGCC;CE=1.71722;CONSBP=38 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-9.03064,-137.98:90:PASS:10984:16771:10498:2:0:0:48:2 +Chromosome 3737466 DEL00000041 AGCCGCTGCCGCCGGCGCCGCCGGCGCCGCCGCCACC A 1200 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3737502;PE=0;MAPQ=0;CT=3to5;CIPOS=-13,13;CIEND=-13,13;SRMAPQ=60;INSLEN=0;HOMLEN=12;SR=20;SRQ=1;CONSENSUS=CCGTTGCCGCCGCCACCGGCCACGGTGCCGACGGTACCGCCGCCGTTGGGGCCGCCCTGACCGCCGTCGCCGCCGAAGCCGCCCTTGCCGCCGAAAAAGCCGCTGCCGCCTTGGGTGACGGAGCTGTTGCCGCCGACGCCGTCACCGCCGTGGCCACCGTCGCCGCCCTTGCCGCCCTCGCCGGAGCTAAGG;CE=1.76286;CONSBP=98 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-164.976,-16.5328,0:10000:PASS:886:269:617:0:0:0:0:55 +Chromosome 3795054 DEL00000042 T 6840 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3796412;PE=94;MAPQ=60;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=20;SRQ=1;CONSENSUS=CACTGTTTCTATGAGCCGCCGACGCATCTGCACGGCCAGCTCTGGCAGCTGGCTTTCGGGCAATGCCTGCACATCGCAAGGTCCGCCGATCGCGGTAATCAAGTCCCCGCGTCCGTTGCGAATCGTGGTTGTCATTGCGCGCGAACCTGTTTGGGAAGGCCGAATCGCACC;CE=1.95704;CONSBP=96 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-524.924,-52.6042,0:10000:PASS:581:29:484:0:0:94:0:175 +Chromosome 3890775 DEL00000043 G 7258 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3892133;PE=101;MAPQ=60;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=60;INSLEN=0;HOMLEN=4;SR=20;SRQ=1;CONSENSUS=GCTGCGGCCCGACCCCATGAGCGTCGCGTCTGTCCACCGCCATGCAAGAACACCACGGCACGCGCTCGCGGGTCTCCCAAGCGGTCGGCGACGATACGGACACCGCCCGGCCCGTGGACCGAGAACGATTCAGCTGCCATTGATATCGGGTCCATCAGGGGAT;CE=1.90768;CONSBP=98 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-587.915,-58.9167,0:10000:PASS:457:0:593:0:0:101:0:196 +Chromosome 3927522 DEL00000044 AGGCGGCCAAGGCGGCGACGGCGGCACCGGAGGGGCCGGCGGCGCAGGCCCAGTGCTGTTCGGCCACGGCGGCGCCGGCGGCATG A 1080 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3927606;PE=0;MAPQ=0;CT=3to5;CIPOS=-17,17;CIEND=-17,17;SRMAPQ=60;INSLEN=0;HOMLEN=16;SR=18;SRQ=1;CONSENSUS=GGGTTGTTCATGAACGGCGGCGACGGCGGCGCCGGCGGTCAAGGCGGCGACGGTGCGGCCGGCGACGCGGCTGCCAGCGCCGGCGGCACCGGCGGCAAAGGCGGCCAAGGCGGCACCGGTGGAATGGGCGGCGCCGGCGGAGACGGCACCACCGTCATCGCGGCCGGTACCGGGGGGGAGG;CE=1.70241;CONSBP=99 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-147.768,-15.0196,0:150:PASS:1802:929:1360:1:0:0:0:50 +Chromosome 3936503 DEL00000045 CGGCGCCGGCGGCAACGGCGGCTCTGCCACCGGCGTCGGTAACGGCGGTAACGGCGGTGATGGCGGCAACGGCGGCGACGGCGGCAACGGCGCACCCGGCGGCTTCGGTGGCGGCGCT C 600 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3936620;PE=0;MAPQ=0;CT=3to5;CIPOS=-13,13;CIEND=-13,13;SRMAPQ=60;INSLEN=0;HOMLEN=14;SR=10;SRQ=0.994792;CONSENSUS=CGCCAACGGCGGAGCCGGCGGTGCCGGGGGAACGCCCACCGGCAGTGGCACCGAGGGGACCGGCGGCGACGGTGGAGATGCCGGCGCCGGCGGCTTGGGCGGCTCCGGCGCCGGCGGCGGCACCGACGGCGACGACGGCAACGGCGGCAGCCCCGGCACCGACGGCAGCTAAGCTAACGGCAGCCCAAAGCG;CE=1.68535;CONSBP=82 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-128.981,-12.9256,0:129:PASS:2075:512:2927:0:0:0:0:43 +Chromosome 3941342 DEL00000046 ACCGGCGGCACCGGCGGCAACGCCGGCG A 57 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=3941369;PE=0;MAPQ=0;CT=3to5;CIPOS=-14,14;CIEND=-14,14;SRMAPQ=45;INSLEN=0;HOMLEN=17;SR=2;SRQ=0.992188;CONSENSUS=GCTGCTAGCCGCCCAAGACGGCGGCCAAGGCGGCACCGGCGGCGCCGGCTTCACCCAAGGCGCCGACGGCAACGCCGGCAACGGCGGTGACGGCGGGGTCGGCGGCAACGGCGGAAACGGCGCAGACA;CE=1.71832;CONSBP=35 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-11.0199,-134.308:110:PASS:1487:3477:2192:2:0:0:63:4 +Chromosome 4008648 DEL00000047 GGCGACGGCGAGCAGACGCAAAATCGCCCAACACGCCCGCAAAATGGGCGATTTT G 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=4008702;PE=0;MAPQ=0;CT=3to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=60;INSLEN=0;HOMLEN=4;SR=2;SRQ=0.993151;CONSENSUS=CATATTCGCCATCCGCGAGGACAGCTGCCCCAACCACGCGACATACCGGACGTGGCTCACCAGACTGCTTACCGGCGTCTGCTCGCGCCACTAGAGCCAGGTGTCCTGGGTGGTGGTGGTGAGGAAAGCCTCCAGGTCGTCGCGCC;CE=1.93206;CONSBP=74 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-5.68576,0,-44.6801:57:PASS:3866:2232:2274:1:0:0:17:4 +Chromosome 4061782 DEL00000048 GGCCAGCGCCTCCCAGGCCGCCGCGGCA G 180 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=4061809;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=60;INSLEN=0;HOMLEN=10;SR=3;SRQ=0.992248;CONSENSUS=CGACGGCCAGGCCAGTGATCAGAGCGTCGTAGGTGGACGCCGTGGTTTGCAACTCGGCGGCCAGCATCGGTCCCGAACCGGGTCCGGCGTACATCAGCGCGGAGTTGACCTCCGGCGGTAACTGAGCAA;CE=1.92059;CONSBP=59 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-23.1778,-350.949:10000:PASS:2412:4792:2527:2:0:0:122:5 +Chromosome 4221175 DEL00000049 TGCCGAGGTGGCCGCCGGCGCCCGCCGCCTGTCAGCGATCGCCGAACTCACCAGCCGGCGCACCGGCAATGACCAGCGGGCCGACTGGGCGTGCGACGGCTGGGACTGCGCGGCC T 120 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=4221289;PE=0;MAPQ=0;CT=3to5;CIPOS=-17,17;CIEND=-17,17;SRMAPQ=60;INSLEN=0;HOMLEN=16;SR=2;SRQ=1;CONSENSUS=ATGCCGACGATGCCGCGCTGCTTGCCGCAATCGAGGACTGCGCGCGTGCCGAGGTGGCCGCCGCACTGACCGTAAGCCACCGTAAGGCCTCCGGGCAGATGCATCTGA;CE=1.90695;CONSBP=47 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-29.7845,-392.943:10000:PASS:12751:23625:10853:2:0:0:135:4 +Chromosome 4231859 DEL00000050 CGCGGTCTGTGCGCCGGGCGCACGCACCGAATTCGAGCTATTAGCGGCCGCGGCAAGGGACGCATTCGGCCTGGACGTCCACCCAGCGGT C 1200 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.8;END=4231948;PE=0;MAPQ=0;CT=3to5;CIPOS=-14,14;CIEND=-14,14;SRMAPQ=60;INSLEN=0;HOMLEN=18;SR=20;SRQ=1;CONSENSUS=GGCCCGCTGGGCCCGGGAATTGGCAAAGGGTCGCCAGGTTGGTCACATCGTGCTCGCCGCCGCATCGCGTCGATTGCTGCCCTCCGAGGATGACGCGGTCGCGGTATGTGCGCCAGCGGGACGACAACCCGCACCGGGACAGCATGGTGTGGCGCTTCGCCGCCGACACCAATGACCTAGG;CE=1.89818;CONSBP=100 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-404.941,-40.5804,0:10000:PASS:6338:1311:6837:0:0:0:0:135 diff --git a/tests/fixtures/mtuberculosis/converged_who_fohm_tbdb.bed.gz b/tests/fixtures/mtuberculosis/converged_who_fohm_tbdb.bed.gz new file mode 100644 index 0000000000000000000000000000000000000000..168f5ffefe7af3bf84b671e9be4c71f27f18d6d9 GIT binary patch literal 1230 zcmV;<1Tp&`iwFb&00000{{{d;LjnM?1g)0AawEA7hR?{eI8^`v0^m{BOwDBv8|RW+ zs!g@VUDHzcw&clro<0R?V_RN##)sAAmrD2m5ClkWAC~Dbou)$%83n;a4eq`pVur6z z%Pma%ar(Wh!|`T6K2FQ@+v9MY#_8CfZpQxm%fE-|_u=_R9p>fvufJ_yVi;ipLL|Qg z(Fn5ni-SnP>tSW?#FN# 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ABS`W1Qbs z#;qzE6GMn*tDNccx|z+!I%m*P+Tgx*ULiLllO1LXcK21K!BMK(oSaC8j|cwRI?HqO z96C_)YT2ljINQZ{B!i#YOWTl~9C`H2NApv{fwU1t-$Vo8C3Y~rwjyOCVTVuOedR4An~`+G$dNes2caK?y^Yql&e5^AV3>Rkw=BxT}b7p zV@VEFioE%UdsP`}bGOcPDwmra*hSig*v0`4GzRJb5M`Q!7(@*b%cEIZWe|8~&dDNQ z*fCZ&^2p%2Gz6X$p~20*EA%h|Bf(F78Q@D@!3sLMCoPznwtWRcun@&EFBS$xap2(Y zmN&OXZcm77>k<6$L7iJ!^n*skdb2J(Ro@A25sHeJZvP9E8dZ!Zn>l z7AV^sXMJvArW|;wF@suT2EQ5XmmC;{?y8hSJ>o^j(24I(@x&*DMLVR~GO%aO<#4{2 zh!2XNm-EQS0l!-lp#|J~IOB!9r1S;|l8i-cd-NaHB9@CqEOg7 z2+3Ni4yBwy6}wx!>QJYM`rcdeF!a`5%XuU~$1f>osy0}gb${YjsvV2ArG4S%=Al<^ zusdsW8{%a@T4}ck+Bw?~suQ*2BD=MIrMK*dXI&F?&{1k<(^1HE#Qqc0y%-wEY=LqJ zo&=X<_0F002c9)wUk+jMkwrjcS3s0FdJLw^F;ZidoI*wM}7ax>q$7VRGQC2uO6i4bHgF}*^)ddO~l z7_CkO%bdk%ju$Lfj9tU7kv7S0U0__pF}-0t*r8Q1uw>e1yKyWHh*H^CEzdAcPXrL# z0yYkODP-@^fz#5ktXfKK;uch_=?P^|Clo};J{-NYLcu||L5zWjYB}0tJG}Lc=bj>p zy-1y1zy8so{>}T7?C$y+yYNmk!gT82$8m^r?ANV Date: Fri, 22 Mar 2024 14:22:13 +0100 Subject: [PATCH 2/5] Create test for annotate delly --- tests/fixtures/mtuberculosis/__init__.py | 15 +++++++++++ tests/test_cli.py | 32 +++++++++++++++++++++++- 2 files changed, 46 insertions(+), 1 deletion(-) diff --git a/tests/fixtures/mtuberculosis/__init__.py b/tests/fixtures/mtuberculosis/__init__.py index 3fa7b36..449bd4d 100644 --- a/tests/fixtures/mtuberculosis/__init__.py +++ b/tests/fixtures/mtuberculosis/__init__.py @@ -51,3 +51,18 @@ def mtuberculosis_snv_vcf_path(data_path): def mtuberculosis_sv_vcf_path(data_path): """Get path for mtuberculosis meta file""" return str(data_path.joinpath("mtuberculosis", "sv.vcf")) + +@pytest.fixture() +def mtuberculosis_delly_bcf_path(data_path): + """Get path for mtuberculosis meta file""" + return str(data_path.joinpath("mtuberculosis", "delly.bcf")) + +@pytest.fixture() +def converged_bed_path(data_path): + """Get path for mtuberculosis converged who fohm tbdb bgzipped bed file""" + return str(data_path.joinpath("mtuberculosis", "converged_who_fohm_tbdb.bed.gz")) + +@pytest.fixture() +def annotated_delly_path(data_path): + """Get path for annotated delly vcf file""" + return str(data_path.joinpath("mtuberculosis", "annotated_delly.vcf")) diff --git a/tests/test_cli.py b/tests/test_cli.py index 048da8c..f97d02b 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -4,7 +4,7 @@ from click.testing import CliRunner -from prp.cli import create_bonsai_input, create_cdm_input +from prp.cli import create_bonsai_input, create_cdm_input, annotate_delly def test_create_output_saureus( @@ -160,6 +160,36 @@ def test_cdm_input_cmd( assert cmd_output == ecoli_cdm_input +def test_annotate_delly( + mtuberculosis_delly_bcf_path, converged_bed_path, annotated_delly_path +): + """Test command for annotating delly output.""" + runner = CliRunner() + with runner.isolated_filesystem(): + sample_id = "test_mtuberculosis_1" + output_fname = f"{sample_id}_annotated_delly.vcf" + result = runner.invoke( + annotate_delly, + [ + "--vcf", + mtuberculosis_delly_bcf_path, + "--bed", + converged_bed_path, + "--output", + output_fname, + ], + ) + + # test successful execution of command + assert result.exit_code == 0 + + # test correct output format + with open(output_fname, "r", encoding="utf-8") as test_annotated_delly_output, \ + open(annotated_delly_path, "r", encoding="utf-8") as annotated_delly_output: + test_contents = test_annotated_delly_output.read() + expected_contents = annotated_delly_output.read() + assert test_contents == expected_contents + def test_create_output_mtuberculosis( mtuberculosis_analysis_meta_path, From ca116efec4c01b7465448c2ff58298ed9fe1b30b Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Fri, 22 Mar 2024 14:24:49 +0100 Subject: [PATCH 3/5] Update CHANGELOG.md re annotate delly pytest --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1767863..cc4c527 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ - Added `sequencing_run` and `lims_id` to output (bonsai input) - Added function for annotating delly variants intersecting with resistance targets - Added capability of handling empty dictionaries from serotypefinder output + - Added pytest for `prp annotate-delly` ### Fixed From 4741571b8320548ebb89309032a2a9a916ba5e05 Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Mon, 25 Mar 2024 08:58:50 +0100 Subject: [PATCH 4/5] Add pyyaml to bonsai-prp --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ec3bc76..164b022 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,8 @@ dependencies = [ "pandas==2.1.3", "Biopython==1.83", "cyvcf2", - "pysam" + "pysam", + "pyyaml" ] [project.urls] From 28018fbd93dfe887c3c880c0c06bbbe2bf5ca296 Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Mon, 25 Mar 2024 09:00:49 +0100 Subject: [PATCH 5/5] Update CHANGELOG.md re pyyaml --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cc4c527..1f8873e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ - Added function for annotating delly variants intersecting with resistance targets - Added capability of handling empty dictionaries from serotypefinder output - Added pytest for `prp annotate-delly` + - Added `pyyaml` to docker image ### Fixed