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@mbaudis
mbaudis committed Oct 31, 2023
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3 changes: 3 additions & 0 deletions .gitignore
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data/.DS_Store
.DS_Store
156 changes: 156 additions & 0 deletions data/progenetix-test-files/progenetix_variants-2.vcf
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##fileformat=VCFv4.4
##reference=GRCh38
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DEL,Description="Deletion">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record">
##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant">
##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint">
##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER FORMAT INFO pgxbs-kftvjv8w
9 38356923 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=38738623;SVLEN=381701 0/1
7 50258 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=1552361;SVLEN=1502104 0/1
10 107636784 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=109576103;SVLEN=1939320 0/1
11 88712752 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=91791316;SVLEN=3078565 0/1
3 52550772 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=60342869;SVLEN=7792098 0/1
3 178174186 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=178947684;SVLEN=773499 0/1
4 52267243 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=57738815;SVLEN=5471573 0/1
12 26548974 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=57762727;SVLEN=31213754 0/1
13 20673027 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=22206640;SVLEN=1533614 0/1
11 27639380 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=27937415;SVLEN=298036 0/1
14 82048826 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=85571197;SVLEN=3522372 0/1
6 165392 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=14564131;SVLEN=14398740 0/1
12 19893956 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=25647080;SVLEN=5753125 0/1
10 66016 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=38663748;SVLEN=38597733 0/1
7 55475198 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=159333942;SVLEN=103858745 0/1
22 28015761 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=28437514;SVLEN=421754 0/1
11 91792344 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=94304393;SVLEN=2512050 0/1
4 101910129 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=189854489;SVLEN=87944361 0/1
5 91536579 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=97427144;SVLEN=5890566 0/1
9 80365648 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=80506749;SVLEN=141102 0/1
11 102302127 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=135074876;SVLEN=32772750 0/1
1 239310256 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=248874237;SVLEN=9563982 0/1
3 168884033 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=172762057;SVLEN=3878025 0/1
20 31367645 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=64272376;SVLEN=32904732 0/1
22 37008127 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=44285326;SVLEN=7277200 0/1
7 53966783 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=55424205;SVLEN=1457423 0/1
2 79005162 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=83717168;SVLEN=4712007 0/1
9 135349970 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=138192914;SVLEN=2842945 0/1
5 133295968 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=143578199;SVLEN=10282232 0/1
9 9284467 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=9489179;SVLEN=204713 0/1
1 238779038 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=239306551;SVLEN=527514 0/1
9 9517018 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=9533062;SVLEN=16045 0/1
16 63648593 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=64838324;SVLEN=1189732 0/1
1 210805144 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=212919691;SVLEN=2114548 0/1
12 88750297 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=133182808;SVLEN=44432512 0/1
16 78168924 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=78518631;SVLEN=349708 0/1
16 66330851 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=71033895;SVLEN=4703045 0/1
21 40198068 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=40794521;SVLEN=596454 0/1
7 36664688 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=53954470;SVLEN=17289783 0/1
18 10010886 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=10085162;SVLEN=74277 0/1
22 47275458 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=49115759;SVLEN=1840302 0/1
11 7931063 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=10855574;SVLEN=2924512 0/1
11 34978812 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=36597125;SVLEN=1618314 0/1
19 38044369 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=39150506;SVLEN=1106138 0/1
6 169657765 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=170596889;SVLEN=939125 0/1
7 1574626 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=1881190;SVLEN=306565 0/1
14 49341504 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=76867509;SVLEN=27526006 0/1
3 119571862 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=141655831;SVLEN=22083970 0/1
1 116915243 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=210784951;SVLEN=93869709 0/1
2 83751989 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=129805593;SVLEN=46053605 0/1
2 133193090 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=141004396;SVLEN=7811307 0/1
3 60352182 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=61057116;SVLEN=704935 0/1
10 104216695 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=107621134;SVLEN=3404440 0/1
4 1816868 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=7496148;SVLEN=5679281 0/1
2 78454403 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=78997591;SVLEN=543189 0/1
22 25965362 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=27051335;SVLEN=1085974 0/1
11 12547573 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=14615845;SVLEN=2068273 0/1
3 141656391 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=141698179;SVLEN=41789 0/1
3 8764846 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=16683814;SVLEN=7918969 0/1
10 63637958 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=63939719;SVLEN=301762 0/1
2 20579871 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=78413168;SVLEN=57833298 0/1
11 72287282 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=78024098;SVLEN=5736817 0/1
9 119895902 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=135326011;SVLEN=15430110 0/1
1 93732957 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=94754624;SVLEN=1021668 0/1
11 22364645 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=26127706;SVLEN=3763062 0/1
1 817187 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=4076982;SVLEN=3259796 0/1
3 94158167 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=99608762;SVLEN=5450596 0/1
18 10811479 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=48739803;SVLEN=37928325 0/1
18 936561 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=2137472;SVLEN=1200912 0/1
3 141706577 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=160763505;SVLEN=19056929 0/1
18 2572058 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=3042418;SVLEN=470361 0/1
2 132674654 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=133176270;SVLEN=501617 0/1
9 9579105 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=9639926;SVLEN=60822 0/1
5 57489270 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=64094571;SVLEN=6605302 0/1
7 1881433 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=3184559;SVLEN=1303127 0/1
6 24009567 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=32249590;SVLEN=8240024 0/1
5 30784521 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=38732159;SVLEN=7947639 0/1
11 45023639 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=48548881;SVLEN=3525243 0/1
22 16396409 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=16792288;SVLEN=395880 0/1
22 32652231 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=36984339;SVLEN=4332109 0/1
4 10140743 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=10613359;SVLEN=472617 0/1
8 13959288 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=17582298;SVLEN=3623011 0/1
9 9640336 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=10606301;SVLEN=965966 0/1
11 61162405 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=67708154;SVLEN=6545750 0/1
2 12995 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=19679302;SVLEN=19666308 0/1
6 14739752 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=24003226;SVLEN=9263475 0/1
3 67392395 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=93962645;SVLEN=26570251 0/1
12 57168 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=186359;SVLEN=129192 0/1
11 19394937 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=22348526;SVLEN=2953590 0/1
9 10617851 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=22525700;SVLEN=11907850 0/1
7 28990631 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=36662665;SVLEN=7672035 0/1
11 10887629 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=11194163;SVLEN=306535 0/1
11 34870184 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=34976467;SVLEN=106284 0/1
3 61057232 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=67379931;SVLEN=6322700 0/1
2 141074771 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=141469263;SVLEN=394493 0/1
5 38848712 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=45841837;SVLEN=6993126 0/1
14 81656972 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=82047207;SVLEN=390236 0/1
9 38742425 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=68570999;SVLEN=29828575 0/1
10 69372494 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=75075224;SVLEN=5702731 0/1
2 129822328 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=132668287;SVLEN=2845960 0/1
18 160888 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=444687;SVLEN=283800 0/1
8 23351280 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=43215871;SVLEN=19864592 0/1
5 162768328 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=163061004;SVLEN=292677 0/1
8 139552853 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=142682583;SVLEN=3129731 0/1
21 10592438 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=25263965;SVLEN=14671528 0/1
1 212921216 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=238760465;SVLEN=25839250 0/1
5 112598 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=30759372;SVLEN=30646775 0/1
7 28280344 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=28973724;SVLEN=693381 0/1
6 116698394 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=116945826;SVLEN=247433 0/1
8 130140822 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=130274811;SVLEN=133990 0/1
19 23821159 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=38035543;SVLEN=14214385 0/1
8 17584628 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=17607353;SVLEN=22726 0/1
5 38748164 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=38801213;SVLEN=53050 0/1
3 4227172 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=4302619;SVLEN=75448 0/1
11 94324688 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=102295451;SVLEN=7970764 0/1
4 19667755 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=23035329;SVLEN=3367575 0/1
8 83221704 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=109182978;SVLEN=25961275 0/1
18 2176171 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=2535815;SVLEN=359645 0/1
5 45857028 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=57458769;SVLEN=11601742 0/1
5 108518530 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=110075621;SVLEN=1557092 0/1
18 3067281 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=7355240;SVLEN=4287960 0/1
3 172844745 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=178173951;SVLEN=5329207 0/1
11 11228097 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=12533074;SVLEN=1304978 0/1
8 17610295 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=21739263;SVLEN=4128969 0/1
11 29010337 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=33968611;SVLEN=4958275 0/1
7 3988721 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=8382034;SVLEN=4393314 0/1
11 2848936 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=7926661;SVLEN=5077726 0/1
18 49092459 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=80246026;SVLEN=31153568 0/1
6 14566228 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=14738367;SVLEN=172140 0/1
10 109591955 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=132747092;SVLEN=23155138 0/1
18 2168297 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=2168672;SVLEN=376 0/1
14 88856866 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=106838890;SVLEN=17982025 0/1
4 10613420 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=19660153;SVLEN=9046734 0/1
10 54114944 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=56263586;SVLEN=2148643 0/1
12 209542 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=3460236;SVLEN=3250695 0/1
11 83544683 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=88712654;SVLEN=5167972 0/1
14 19734967 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=21094401;SVLEN=1359435 0/1
9 6912768 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=7015397;SVLEN=102630 0/1
9 32709066 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=38343509;SVLEN=5634444 0/1
2 141488379 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=237428159;SVLEN=95939781 0/1
6 63622199 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=69508812;SVLEN=5886614 0/1
4 57749997 . . <DEL> . PASS GT IMPRECISE;SVCLAIM=D;END=96519256;SVLEN=38769260 0/1
14 21102115 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=38722184;SVLEN=17620070 0/1
14 76867621 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=81654983;SVLEN=4787363 0/1
12 25658192 . . <DUP> . PASS GT IMPRECISE;SVCLAIM=D;END=26548239;SVLEN=890048 0/1
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