delly Differences observed in VCF files between Delly v1.5.0 and v1.7.2

Hello!

After updating Delly from v1.5.0 to v1.7.2, significant differences were observed in the VCF files generated for the same sample.

The command used for both versions:

delly call -x human.hg38.excl.tsv -g GRCh38.d1.vd1.fa sample.bam

Overall, there are approximately 2826 lines changed out of about 37,000 total records

For example, some variants present in v1.5.0 (e.g. INV00002476, INV00002129, INV00002219, DUP00015556) disappeared, while new variants appeared in v1.7.2 (e.g. BND00037261, BND00039914, DEL00030967).

Differences Delly v1.5.0 (left) vs v1.7.2 (right):

chr2: SNV IDs changed

All chromosomes: Values in fields GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV changed

Could you please clarify the reasons for these differences? Are they expected changes due to updates in the algorithm or parameters? Also, we noticed that Delly runs about 3,5 times faster now - thank you for the improvement!

Nov 11 '25 14:11 Anastasiabum

Yes, the main objective was to improve delly's runtime for deep-coverage and multi-region sequencing. In order to achieve this, I changed the alignment algorithm in the genotyping module, which is why the output of delly v1.7.2 isn't 100% identical to the previous version, but very similar. In my benchmarks less than 1 in 1,000 SV sites (<0.1%) differ from the old version if you ignore the ID column (which is random) and these were mostly low-quality SVs. For the FORMAT fields, the situation is different as the quality scoring is alignment dependent and thus, the GLs and GQs are different. However, if you restrict the comparison to the main GT field results are again very similar to the previous version. Thus, I hope the results are generally comparable at greatly improved runtime. However, if you observe the disappearance of known or even validated (somatic) SVs, I would be very interested to know, in order to ensure that all changes I made to the code were valid. Thank you!

Nov 11 '25 14:11 tobiasrausch

Thank you for detailed explanation, we'll look into our data and check if:

Most of GTs are same
Most differences are in low-quality SVs

We'll come back with test results, but even minor tag/release description will be helpful in the future, left alone full changelog.

Nov 11 '25 15:11 Stikus

We've checked differences and get a lot more, than expected (0.1%);

We've got approximately 300 new/lost SV's between version (from 37k total) and if we examine same SVs (by CHROM, POS, REF, ALT, QUAL, FILTER columns - 36311 total same SVs) - we've got 300+ different GTs for PASS variants and 600+ different GTs for LowQual variants.

Here are some examples of different GTs for PASS variants:

$ cut --complement -f3  delly_v1.7.2.vcf | grep -F -f <(comm -23 <(grep -v '^#' delly_v1.7.2.vcf | cut -f1,2,4,5,6,7,10 | sed -E 's|(^.*\s[0-9]/[0-9]):.*|\1|' | tr '\t' '_' | sort | grep -F -f <(comm -12 <(grep -v '^#' delly_v1.7.2.vcf | cut -f1,2,4,5 | tr '\t' '_' | sort) <(grep -v '^#' delly_v1.5.0.vcf | cut -f1,2,4,5 | tr '\t' '_' | sort))) <(grep -v '^#' delly_v1.5.0.vcf | cut -f1,2,4,5,6,7,10 | sed -E 's|(^.*\s[0-9]/[0-9]):.*|\1|' | tr '\t' '_' | sort | grep -F -f <(comm -12 <(grep -v '^#' delly_v1.7.2.vcf | cut -f1,2,4,5 | tr '\t' '_' | sort) <(grep -v '^#' delly_v1.5.0.vcf | cut -f1,2,4,5 | tr '\t' '_' | sort))) | grep 'PASS' | sort -V | head -n20 | tr '_' '\t' | cut -f1-6)
chr1    984611  C       CTTTATTTCTTTCTTTCTTTCTTTCTTTCT  480     PASS    PRECISE;SVTYPE=INS;END=984611;SVLEN=29;PE=0;MAPQ=0;CT=NtoN;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=59;INSLEN=29;HOMLEN=9;SR=10;SRQ=0.979592;CONSENSUS=GGGTACAGCCGCAAACAATGTACACAGCTGCGGAATTATTTTTCTTTCTTTTTTCTTTTCTTTCTTTTTTCCTTCTTTATTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTGAGATGGGGTTTCGCTCTGTCGCCCAG;CE=1.67689;CONSBP=75    GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-155.385,-9.91865,0:99:PASS:22546:46605:24059:2:0:0:0:33
chr1    5736364 GATAGATAGATAGATAGATAGATAGATACATACATACATACATACATAC       G       240     PASS    PRECISE;SVTYPE=DEL;END=5736412;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=60;INSLEN=0;HOMLEN=9;SR=4;SRQ=1;CONSENSUS=AGAGAGAGATGGGTGGGTGGATGGATGGGATGGATGGATGGATGATGGATGGACAGATGATAGATAGATAGATAGATAGATACATACATACATACATACATACATAGATGAATAGGTGGATAGATGAATGGATAGATAGATAGACAAAGGCATAGCT;CE=1.79263;CONSBP=79 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-193.361,0,-0.56197:7:LowQual:655:751:848:1:0:0:2:36
chr1    24219284        G       GCTTGCTTTCTTTCTTTCTTTCTTTCTTTCTTT       300     PASS    PRECISE;SVTYPE=INS;END=24219284;SVLEN=32;PE=0;MAPQ=0;CT=NtoN;CIPOS=-22,22;CIEND=-22,22;SRMAPQ=40;INSLEN=32;HOMLEN=24;SR=7;SRQ=1;CONSENSUS=CTTCCCCTTCCTTCTTTGTTTCTTTCTTTGTTGCTTGCTTGCTTGCTTGCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTTTCTTTCTTTCCTTTTTTATTTTTTTTGACAGAGTCTCACTCTGTTGCCC;CE=1.38153;CONSBP=45       GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-94.1965,-7.22118,0:72:PASS:13113:36687:23574:2:0:0:0:24
chr1    24859772        A       ACACACACACACACACACATATATTTATT   338     PASS    PRECISE;SVTYPE=INS;END=24859772;SVLEN=28;PE=0;MAPQ=0;CT=NtoN;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=46;INSLEN=28;HOMLEN=1;SR=7;SRQ=1;CONSENSUS=GGTGCACGCCATAATGCCGGCTGCCCAGCTAATTTTAATTAATACACACACACACACACACACACACACACACACACACACATATATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATAGAGATGAGGTTTCACCATGTTGCCCAG;CE=1.88601;CONSBP=64    GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-244.182,-8.9411,0:89:PASS:25955:42909:16954:2:0:0:4:59
chr1    41824773        ATATATATATATAGAGAGAGAGAGAGAGAGAG        A       240     PASS    PRECISE;SVTYPE=DEL;END=41824804;PE=0;MAPQ=0;CT=3to5;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=60;INSLEN=0;HOMLEN=0;SR=4;SRQ=0.983146;CONSENSUS=CATTTATATCACCAGATACCAAGCCCTGTTCCAAGTTAAATATATATATATATATATATATATATATATAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTTTATATATAGAGAGAGAGACAGAGACAGAGAGAGAAAGAGAGACAGAGAGATTGAGTTTTGCTCTTGTT;CE=1.83353;CONSBP=70      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-0.919401,-76.7033:10:LowQual:394:486:281:1:0:0:17:2
chr1    57781124        CTCTATATATATATATATATATATATATA   C       360     PASS    PRECISE;SVTYPE=DEL;END=57781152;PE=0;MAPQ=0;CT=3to5;CIPOS=-20,20;CIEND=-20,20;SRMAPQ=60;INSLEN=0;HOMLEN=20;SR=6;SRQ=0.989848;CONSENSUS=AACTCTTTTGTTCTATGCATATTTTATATATTTGAGATCATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATAGTTGCCTAATTACTTTTTCAGTTTGCTTTATAACGTGATTCCATAGTATCAGATTATTGTTAAAGCTGAATAGTTTCCTATCACATAGATACAAACATA;CE=1.79538;CONSBP=79   GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-72.3971,-0.4163,0:5:LowQual:542:547:340:1:0:0:2:18
chr1    58648562        CACACACACACACACACAGAGAGAGAGAGAGAGAGAGAG C       896     PASS    PRECISE;SVTYPE=DEL;END=58648600;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=15;SRQ=1;CONSENSUS=GCAGTGAGCCGAAATCACACCACTGCACTCCAGCCTGGGTGGCACAGTGAGACTGTCTCAAACACACACACACACACACACACACACACACACACACACAGAGAGAGAGAGAGAGAAAGTGGGTTTAAGATGTAGTTATCCCTTAGTGGCTTCCTGCTTCCTTAGCAGGCTACTGACCATCTCACC;CE=1.96082;CONSBP=99  GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-351.718,0,-6.47756:65:PASS:900:678:1023:1:0:0:6:74
chr1    60920100        CTTTTTTTTTTTTTTTTTTTTTTTTTTTT   C       480     PASS    PRECISE;SVTYPE=DEL;END=60920128;PE=0;MAPQ=0;CT=3to5;CIPOS=-24,24;CIEND=-24,24;SRMAPQ=60;INSLEN=0;HOMLEN=26;SR=8;SRQ=0.984615;CONSENSUS=GGCCAGAACTGGTTCCATCAAGAGTTGTATTCCCTTGTTATCTGCTGCATACATCAAGCGCACGAACACACATACACTTTCTTTTTTTTTTTTTTTTTTTTTTTGAGCTGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGCAGTGCCATCTCAGCTCACTGCAACCTCCGCCTCCTGGGTTCAAAAAATTAT;CE=1.95939;CONSBP=81      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-70.0989,-1.71506,0:17:PASS:462:666:327:2:0:0:1:15
chr1    69608854        CTCTCTCTCTCTCTATATATATATATA     C       180     PASS    PRECISE;SVTYPE=DEL;END=69608880;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=3;SRQ=0.980392;CONSENSUS=ATTTTACCTAACTAACTTTAAAGTAAGAACTGGCATCTCCTATAAGTTGCTCTGTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATACACACACACACACATATATATAAAAATATAT;CE=1.78034;CONSBP=100      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-202.846,0,-1.13436:11:LowQual:415:416:390:1:0:0:3:49
chr1    113022581       ATATATATATATATATATATATATATATATATTT      A       236     PASS    PRECISE;SVTYPE=DEL;END=113022614;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=4;SRQ=0.993548;CONSENSUS=GGTGTGAGCCACCGTGCCCAGCCTGATAACATTTTTTAAAATAAAGTTTGATTATTGTATTGTATACATATATATATATATATATATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTTTTGCCACCGTCCAGGCTGGAGTAC;CE=1.82579;CONSBP=86  GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-118.07,0,-2.07545:21:PASS:248:287:280:1:0:0:2:27
chr1    154203172       AATATATATATATATATATATATATATATAT A       240     PASS    PRECISE;SVTYPE=DEL;END=154203202;PE=0;MAPQ=0;CT=3to5;CIPOS=-35,35;CIEND=-35,35;SRMAPQ=60;INSLEN=0;HOMLEN=35;SR=4;SRQ=1;CONSENSUS=TAAGACTCTGTCTTAGAGAGACTCTGCCTCAAAAAAAAAAAAAAGTTGTTATCTCTGACTGGGCAAATATATATATATATATATATATATATATATATACTTTGTTGGGAATGACTGTAGTTTTTACTTTTTTTTTTTTCTGAGTCAGAGTCCTGCTCTGT;CE=1.85277;CONSBP=66      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-99.4763,0,-4.57925:46:PASS:252:422:206:2:0:0:2:21
chr1    176991413       CAAAAAAAAAAAAAAAAAAAAACCAAA     C       600     PASS    PRECISE;SVTYPE=DEL;END=176991439;PE=0;MAPQ=0;CT=3to5;CIPOS=-19,19;CIEND=-19,19;SRMAPQ=60;INSLEN=0;HOMLEN=18;SR=10;SRQ=0.995192;CONSENSUS=AATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCATGCCATTGCACTCCAGCCTGGGCAACAAACGCTAAACTCTGTCTCAAAAAAAAAAAAAGAAAAACCAACAACAAAACAAAAAGAAACGCTATAGAGCCATAATGAGTGGCTGTCCAAAGCTGGAAAGAAAGAGAATTAAAACGGAGATGAAGTGATGTAGAAC;CE=1.88609;CONSBP=90       GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-148.395,-6.4253,0:64:PASS:375:287:397:1:0:0:1:29
chr1    206743927       TTTCTTTCTTTCTTTCTCTTTCTTTCCTTCC T       129     PASS    PRECISE;SVTYPE=DEL;END=206743957;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=40;INSLEN=0;HOMLEN=9;SR=4;SRQ=1;CONSENSUS=TTTGAGTTTTGTTCACATGTCACTTTTCTCTTTCTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCTTTCTTTCTTTCTT;CE=1.20255;CONSBP=92   GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-73.7272,-1.47653,0:15:PASS:378:380:280:1:0:0:3:20
chr1    213119425       CATATATATATATATATATATATATATATATATATATATATATAT   C       180     PASS    PRECISE;SVTYPE=DEL;END=213119469;PE=0;MAPQ=0;CT=3to5;CIPOS=-32,32;CIEND=-32,32;SRMAPQ=60;INSLEN=0;HOMLEN=31;SR=3;SRQ=0.993464;CONSENSUS=GCCTGAACCATGGGGGTGGAGGTTGCAGTGAGCCAAGATCACGCCACTGCACTCCAGCCTGGGCATATATATATATATATATATATATATATATGAGAGTATTCAATGAGGAGTGCAATAGTCAGAAATGAAGAATGTTTCTTTTCTCTATTT;CE=1.95823;CONSBP=64       GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-61.9846,0,-0.585434:7:LowQual:347:307:307:1:0:0:1:14
chr2    11538629        CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT        C       180     PASS    PRECISE;SVTYPE=DEL;END=11538684;PE=0;MAPQ=0;CT=3to5;CIPOS=-20,20;CIEND=-20,20;SRMAPQ=60;INSLEN=0;HOMLEN=22;SR=3;SRQ=0.986486;CONSENSUS=TTGTTGAATTAGGATTTGATCAGGAGTCCTGGATTCGTAAGAGTCAATTGCAACAGGGATGTAAAGAGAGCTCTGGACAGGAGCTTGTGTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTCCCTCCCTCCCTCCCTTCCTCCCTCCCC;CE=1.93707;CONSBP=109     GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-52.0989,-3.00918,0:30:PASS:805:290:394:0:0:0:0:10
chr2    16665870        G       <INV>   480     PASS    PRECISE;SVTYPE=INV;END=32916332;PE=0;MAPQ=0;CT=3to3;CIPOS=-9,9;CIEND=-9,9;SRMAPQ=60;INSLEN=0;HOMLEN=8;SR=8;SRQ=0.955882;CONSENSUS=GCCCCAGCCGCGCCGCGCTCACCGAGTCGCCGCCGCCCTGCTCTGCCGCCCGCTCCGCCGCCGCCGAGTACGCCTCTCCCGCGGCCGCCGCAGCCTGCGAGACGGCCTCGGAGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGCCGCGGCGCCCCCCCCCCCCCCCCCCCCCCCGGG;CE=1.27947;CONSBP=113  GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-48.8758,0,-76.3998:10000:PASS:1136779:2275426:1095853:2:0:0:85:13
chr2    17477949        GAAAGAAAGAAAGAAGAAAGAAATAAAGA   G       900     PASS    PRECISE;SVTYPE=DEL;END=17477977;PE=0;MAPQ=0;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SRMAPQ=60;INSLEN=0;HOMLEN=12;SR=15;SRQ=0.994152;CONSENSUS=AGAAACCACTTGTGCCCCTAAAGCTATTGAAATGAAAAAGAAAGAAGAAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGAAAGAAATAAAGAAAGAAAGAAAGAAAGAAAGAAAAAAGAAAAGAAAAGAAAAGAAAGGAGGGAGGGAGGAAGGGAGGAAGGG;CE=1.37243;CONSBP=85     GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-218.153,0,-7.65373:77:PASS:464:417:386:1:0:0:4:42
chr2    32916230        G       <DUP>   169     PASS    PRECISE;SVTYPE=DUP;END=149122556;PE=0;MAPQ=0;CT=5to3;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=53;INSLEN=0;HOMLEN=0;SR=4;SRQ=0.975;CONSENSUS=TTGGTACATATGTATACATGTTCCATGTTGGTGTGCTGCACCCATTAACTCGTCATTTACATTAGTTATTCCTCCTAATGCTGGGGGGGGGGGGGGGGGGGGCGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGCGGG;CE=1.701;CONSBP=82   GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-78.9263,0,-23.1497:10000:PASS:4608593:15353740:7796321:2:0:0:10:65
chr2    32916233        G       <DUP>   160     PASS    PRECISE;SVTYPE=DUP;END=62208208;PE=0;MAPQ=0;CT=5to3;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=23;INSLEN=0;HOMLEN=0;SR=6;SRQ=0.983051;CONSENSUS=TGTGAAAATAGTCTCCTTGTTTGTATGTGTCTGTAGACATGAGGAGCCCACATAACAGACAACAGATTCCTCCTTCCTGGGGGGGGTGGGGGGTGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG;CE=1.54403;CONSBP=78      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-2.39525,0,-21.9952:24:PASS:2056361:3976132:2023125:2:0:0:6:2
chr2    32916240        G       <DUP>   127     PASS    PRECISE;SVTYPE=DUP;END=185921835;PE=0;MAPQ=0;CT=5to3;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=60;INSLEN=0;HOMLEN=1;SR=3;SRQ=0.974026;CONSENSUS=GTGCCATGCTGGTGTGCTGCACCCATTAACTCGTCATTTAGCATTAGGTGTATCTCCCAATGCTGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGCGGGCGG;CE=1.48045;CONSBP=64    GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-400.424,-24.137,0:10000:PASS:4608594:20289642:7755803:3:0:0:22:228


$ cut --complement -f3  delly_v1.5.0.vcf | grep -F -f <(comm -23 <(grep -v '^#' delly_v1.7.2.vcf | cut -f1,2,4,5,6,7,10 | sed -E 's|(^.*\s[0-9]/[0-9]):.*|\1|' | tr '\t' '_' | sort | grep -F -f <(comm -12 <(grep -v '^#' delly_v1.7.2.vcf | cut -f1,2,4,5 | tr '\t' '_' | sort) <(grep -v '^#' delly_v1.5.0.vcf | cut -f1,2,4,5 | tr '\t' '_' | sort))) <(grep -v '^#' delly_v1.5.0.vcf | cut -f1,2,4,5,6,7,10 | sed -E 's|(^.*\s[0-9]/[0-9]):.*|\1|' | tr '\t' '_' | sort | grep -F -f <(comm -12 <(grep -v '^#' delly_v1.7.2.vcf | cut -f1,2,4,5 | tr '\t' '_' | sort) <(grep -v '^#' delly_v1.5.0.vcf | cut -f1,2,4,5 | tr '\t' '_' | sort))) | grep 'PASS' | sort -V | head -n20 | tr '_' '\t' | cut -f1-6)
chr1    984611  C       CTTTATTTCTTTCTTTCTTTCTTTCTTTCT  480     PASS    PRECISE;SVTYPE=INS;END=984611;SVLEN=29;PE=0;MAPQ=0;CT=NtoN;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=59;INSLEN=29;HOMLEN=9;SR=10;SRQ=0.979592;CONSENSUS=GGGTACAGCCGCAAACAATGTACACAGCTGCGGAATTATTTTTCTTTCTTTTTTCTTTTCTTTCTTTTTTCCTTCTTTATTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTGAGATGGGGTTTCGCTCTGTCGCCCAG;CE=1.67689;CONSBP=75    GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-83.9515,0,-46.9727:10000:PASS:22546:46605:24059:2:0:0:19:33
chr1    5736364 GATAGATAGATAGATAGATAGATAGATACATACATACATACATACATAC       G       240     PASS    PRECISE;SVTYPE=DEL;END=5736412;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=60;INSLEN=0;HOMLEN=9;SR=4;SRQ=1;CONSENSUS=AGAGAGAGATGGGTGGGTGGATGGATGGGATGGATGGATGGATGATGGATGGACAGATGATAGATAGATAGATAGATAGATACATACATACATACATACATACATAGATGAATAGGTGGATAGATGAATGGATAGATAGATAGACAAAGGCATAGCT;CE=1.79263;CONSBP=79 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-117.794,-4.63281,0:46:PASS:655:751:848:1:0:0:2:36
chr1    24219284        G       GCTTGCTTTCTTTCTTTCTTTCTTTCTTTCTTT       300     PASS    PRECISE;SVTYPE=INS;END=24219284;SVLEN=32;PE=0;MAPQ=0;CT=NtoN;CIPOS=-22,22;CIEND=-22,22;SRMAPQ=40;INSLEN=32;HOMLEN=24;SR=7;SRQ=1;CONSENSUS=CTTCCCCTTCCTTCTTTGTTTCTTTCTTTGTTGCTTGCTTGCTTGCTTGCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTTTCTTTCTTTCCTTTTTTATTTTTTTTGACAGAGTCTCACTCTGTTGCCC;CE=1.38153;CONSBP=45       GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-68.8695,0,-15.8736:157:PASS:13113:36687:23574:2:0:0:8:24
chr1    24859772        A       ACACACACACACACACACATATATTTATT   338     PASS    PRECISE;SVTYPE=INS;END=24859772;SVLEN=28;PE=0;MAPQ=0;CT=NtoN;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=46;INSLEN=28;HOMLEN=1;SR=7;SRQ=1;CONSENSUS=GGTGCACGCCATAATGCCGGCTGCCCAGCTAATTTTAATTAATACACACACACACACACACACACACACACACACACACACATATATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATAGAGATGAGGTTTCACCATGTTGCCCAG;CE=1.88601;CONSBP=64    GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-168.438,0,-1.25683:13:LowQual:25955:42909:16954:2:0:0:6:56
chr1    41824773        ATATATATATATAGAGAGAGAGAGAGAGAGAG        A       240     PASS    PRECISE;SVTYPE=DEL;END=41824804;PE=0;MAPQ=0;CT=3to5;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=60;INSLEN=0;HOMLEN=0;SR=4;SRQ=0.983146;CONSENSUS=CATTTATATCACCAGATACCAAGCCCTGTTCCAAGTTAAATATATATATATATATATATATATATATATAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTTTATATATAGAGAGAGAGACAGAGACAGAGAGAGAAAGAGAGACAGAGAGATTGAGTTTTGCTCTTGTT;CE=1.83353;CONSBP=70      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-1.18499,0,-50.7808:12:LowQual:394:486:281:1:0:0:17:2
chr1    57781124        CTCTATATATATATATATATATATATATA   C       360     PASS    PRECISE;SVTYPE=DEL;END=57781152;PE=0;MAPQ=0;CT=3to5;CIPOS=-20,20;CIEND=-20,20;SRMAPQ=60;INSLEN=0;HOMLEN=20;SR=6;SRQ=0.989848;CONSENSUS=AACTCTTTTGTTCTATGCATATTTTATATATTTGAGATCATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATAGTTGCCTAATTACTTTTTCAGTTTGCTTTATAACGTGATTCCATAGTATCAGATTATTGTTAAAGCTGAATAGTTTCCTATCACATAGATACAAACATA;CE=1.79538;CONSBP=79   GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-54.8797,0,-0.882998:10:LowQual:542:547:340:1:0:0:2:18
chr1    58648562        CACACACACACACACACAGAGAGAGAGAGAGAGAGAGAG C       896     PASS    PRECISE;SVTYPE=DEL;END=58648600;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=15;SRQ=1;CONSENSUS=GCAGTGAGCCGAAATCACACCACTGCACTCCAGCCTGGGTGGCACAGTGAGACTGTCTCAAACACACACACACACACACACACACACACACACACACACAGAGAGAGAGAGAGAGAAAGTGGGTTTAAGATGTAGTTATCCCTTAGTGGCTTCCTGCTTCCTTAGCAGGCTACTGACCATCTCACC;CE=1.96082;CONSBP=99  GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-235.734,-3.01563,0:30:PASS:900:678:1023:1:0:0:6:74
chr1    60920100        CTTTTTTTTTTTTTTTTTTTTTTTTTTTT   C       480     PASS    PRECISE;SVTYPE=DEL;END=60920128;PE=0;MAPQ=0;CT=3to5;CIPOS=-24,24;CIEND=-24,24;SRMAPQ=60;INSLEN=0;HOMLEN=26;SR=8;SRQ=0.984615;CONSENSUS=GGCCAGAACTGGTTCCATCAAGAGTTGTATTCCCTTGTTATCTGCTGCATACATCAAGCGCACGAACACACATACACTTTCTTTTTTTTTTTTTTTTTTTTTTTGAGCTGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGCAGTGCCATCTCAGCTCACTGCAACCTCCGCCTCCTGGGTTCAAAAAATTAT;CE=1.95939;CONSBP=81      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-45.2818,0,-1.2864:13:LowQual:462:666:327:2:0:0:2:16
chr1    69608854        CTCTCTCTCTCTCTATATATATATATA     C       180     PASS    PRECISE;SVTYPE=DEL;END=69608880;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=3;SRQ=0.980392;CONSENSUS=ATTTTACCTAACTAACTTTAAAGTAAGAACTGGCATCTCCTATAAGTTGCTCTGTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATACACACACACACACATATATATAAAAATATAT;CE=1.78034;CONSBP=100      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-141.106,-4.35886,0:44:PASS:415:416:390:1:0:0:3:49
chr1    113022581       ATATATATATATATATATATATATATATATATTT      A       236     PASS    PRECISE;SVTYPE=DEL;END=113022614;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=4;SRQ=0.993548;CONSENSUS=GGTGTGAGCCACCGTGCCCAGCCTGATAACATTTTTTAAAATAAAGTTTGATTATTGTATTGTATACATATATATATATATATATATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTTTTGCCACCGTCCAGGCTGGAGTAC;CE=1.82579;CONSBP=86  GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-76.7865,-2.01596,0:20:PASS:248:287:280:1:0:0:2:27
chr1    154203172       AATATATATATATATATATATATATATATAT A       240     PASS    PRECISE;SVTYPE=DEL;END=154203202;PE=0;MAPQ=0;CT=3to5;CIPOS=-35,35;CIEND=-35,35;SRMAPQ=60;INSLEN=0;HOMLEN=35;SR=4;SRQ=1;CONSENSUS=TAAGACTCTGTCTTAGAGAGACTCTGCCTCAAAAAAAAAAAAAAGTTGTTATCTCTGACTGGGCAAATATATATATATATATATATATATATATATATACTTTGTTGGGAATGACTGTAGTTTTTACTTTTTTTTTTTTCTGAGTCAGAGTCCTGCTCTGT;CE=1.85277;CONSBP=66      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-59.6933,-0.116614,0:4:LowQual:252:422:206:2:0:0:2:21
chr1    176991413       CAAAAAAAAAAAAAAAAAAAAACCAAA     C       600     PASS    PRECISE;SVTYPE=DEL;END=176991439;PE=0;MAPQ=0;CT=3to5;CIPOS=-19,19;CIEND=-19,19;SRMAPQ=60;INSLEN=0;HOMLEN=18;SR=10;SRQ=0.995192;CONSENSUS=AATCGCTTGAACCTGGGAGGCGAAGGTTGCAGTGAGCCGAGATCATGCCATTGCACTCCAGCCTGGGCAACAAACGCTAAACTCTGTCTCAAAAAAAAAAAAAGAAAAACCAACAACAAAACAAAAAGAAACGCTATAGAGCCATAATGAGTGGCTGTCCAAAGCTGGAAAGAAAGAGAATTAAAACGGAGATGAAGTGATGTAGAAC;CE=1.88609;CONSBP=90       GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-98.6618,0,-1.67046:17:PASS:375:287:397:1:0:0:4:34
chr1    206743927       TTTCTTTCTTTCTTTCTCTTTCTTTCCTTCC T       129     PASS    PRECISE;SVTYPE=DEL;END=206743957;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=40;INSLEN=0;HOMLEN=9;SR=4;SRQ=1;CONSENSUS=TTTGAGTTTTGTTCACATGTCACTTTTCTCTTTCTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCTTTCTTTCTTTCTT;CE=1.20255;CONSBP=92   GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-33.1083,0,-17.2725:10000:PASS:378:380:280:1:0:0:8:14
chr1    213119425       CATATATATATATATATATATATATATATATATATATATATATAT   C       180     PASS    PRECISE;SVTYPE=DEL;END=213119469;PE=0;MAPQ=0;CT=3to5;CIPOS=-32,32;CIEND=-32,32;SRMAPQ=60;INSLEN=0;HOMLEN=31;SR=3;SRQ=0.993464;CONSENSUS=GCCTGAACCATGGGGGTGGAGGTTGCAGTGAGCCAAGATCACGCCACTGCACTCCAGCCTGGGCATATATATATATATATATATATATATATATGAGAGTATTCAATGAGGAGTGCAATAGTCAGAAATGAAGAATGTTTCTTTTCTCTATTT;CE=1.95823;CONSBP=64       GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-50.2969,-1.61432,0:16:PASS:347:307:307:1:0:0:1:16
chr2    11538629        CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT        C       180     PASS    PRECISE;SVTYPE=DEL;END=11538684;PE=0;MAPQ=0;CT=3to5;CIPOS=-20,20;CIEND=-20,20;SRMAPQ=60;INSLEN=0;HOMLEN=22;SR=3;SRQ=0.986486;CONSENSUS=TTGTTGAATTAGGATTTGATCAGGAGTCCTGGATTCGTAAGAGTCAATTGCAACAGGGATGTAAAGAGAGCTCTGGACAGGAGCTTGTGTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTCCCTCCCTCCCTCCCTTCCTCCCTCCCC;CE=1.93707;CONSBP=109     GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-29.6833,0,-19.7843:10000:PASS:805:290:394:0:0:0:7:10
chr2    16665870        G       <INV>   480     PASS    PRECISE;SVTYPE=INV;END=32916332;PE=0;MAPQ=0;CT=3to3;CIPOS=-9,9;CIEND=-9,9;SRMAPQ=60;INSLEN=0;HOMLEN=8;SR=8;SRQ=0.955882;CONSENSUS=GCCCCAGCCGCGCCGCGCTCACCGAGTCGCCGCCGCCCTGCTCTGCCGCCCGCTCCGCCGCCGCCGAGTACGCCTCTCCCGCGGCCGCCGCAGCCTGCGAGACGGCCTCGGAGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGCCGCGGCGCCCCCCCCCCCCCCCCCCCCCCCGGG;CE=1.27947;CONSBP=113  GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-19.9848,-282.535:10000:PASS:1136779:2275426:1095853:2:0:0:235:15
chr2    17477949        GAAAGAAAGAAAGAAGAAAGAAATAAAGA   G       900     PASS    PRECISE;SVTYPE=DEL;END=17477977;PE=0;MAPQ=0;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SRMAPQ=60;INSLEN=0;HOMLEN=12;SR=15;SRQ=0.994152;CONSENSUS=AGAAACCACTTGTGCCCCTAAAGCTATTGAAATGAAAAAGAAAGAAGAAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGAAAGAAATAAAGAAAGAAAGAAAGAAAGAAAGAAAAAAGAAAAGAAAAGAAAAGAAAGGAGGGAGGGAGGAAGGGAGGAAGGG;CE=1.37243;CONSBP=85     GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-135.558,-2.31057,0:23:PASS:464:417:386:1:0:0:4:48
chr2    32916230        G       <DUP>   169     PASS    PRECISE;SVTYPE=DUP;END=149122556;PE=0;MAPQ=0;CT=5to3;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=53;INSLEN=0;HOMLEN=0;SR=4;SRQ=0.975;CONSENSUS=TTGGTACATATGTATACATGTTCCATGTTGGTGTGCTGCACCCATTAACTCGTCATTTACATTAGTTATTCCTCCTAATGCTGGGGGGGGGGGGGGGGGGGGCGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGCGGG;CE=1.701;CONSBP=82   GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-317.941,-60.2926,0:10000:PASS:4608593:15353740:7796321:2:0:0:1:249
chr2    32916240        G       <DUP>   127     PASS    PRECISE;SVTYPE=DUP;END=185921835;PE=0;MAPQ=0;CT=5to3;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=60;INSLEN=0;HOMLEN=1;SR=3;SRQ=0.974026;CONSENSUS=GTGCCATGCTGGTGTGCTGCACCCATTAACTCGTCATTTAGCATTAGGTGTATCTCCCAATGCTGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGCGGGCGG;CE=1.48045;CONSBP=64    GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-276.595,0,-15.4478:154:PASS:4608594:20289642:7755803:3:0:0:46:204

We doesn't have validated variants, but hope provided variants help. We can add more different variants if you need.

Nov 14 '25 13:11 Stikus

Thanks, yes, some of these differing GTs are due to the fact that the GLs for heterozygous and homozygous variants were already very close to each other due to uneven read support (e.g., REF: 2 reads, ALT: 36 reads). Because of the new quality and alignment scoring, some of these variants have now switched between heterozygous and homozygous (and vice versa), which was to be expected. As soon as I have time, I will re-analyze the GiaB SV dataset to see if delly's GTs have slightly improved or worsened.

Nov 17 '25 15:11 tobiasrausch