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View Code? Open in Web Editor NEWStructural variant VCF annotation, duplicate removal and comparison
License: BSD 3-Clause "New" or "Revised" License
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About the explanation of annotation output
Dear dellytools team,
Thank you for providing the convenient tool "dellytools." Regarding the interpretation of the annotation results, I have some questions and would like to confirm them with you further.
- Example 1, Pmu.1_1G000010(739;+)
Does the first number refer to the position 739 downstream of the gene body, or the position 739 downstream of the translation start site for Pmu.1_1G000010? - Example 2, Pmu.1_1G000110(-947;-)
On the contrary, does Pmu.1_1G000110(-947;-) refer to the position 947 upstream of the gene body, or the translation start site? - Example 3,Pmu.1_1G000120(0;-)
When it's 0, does it refer to being within the gene body, or does it signify something else? - What does "query.ct" mean?
Sincerely yours,
Clarence
sansa annotate error what(): bad lexical cast: source type value could not be interpreted as target
hi
first thank you for provide this beautiful program of art
when i run sansa annotate with my VCF.gz (using delly call and delly filter) and hg38.gtf for gene_id annotation
error thrown like this :
[2021-Mar-31 14:30:16] sansa annotate -i gene_id -g /users/hslee/ref/hg38/hg38.refGene.gtf.gz JSH_LN_Lt.delly.SV.vcf.gz
[2021-Mar-31 14:30:17] Parse SV annotation database
[2021-Mar-31 14:30:17] Parsed 2 out of 2 VCF/BCF records.
[2021-Mar-31 14:30:17] BED feature parsing
terminate called after throwing an instance of 'boost::wrapexcept<boost::bad_lexical_cast>'
what(): bad lexical cast: source type value could not be interpreted as target
stopped (core dumped)
my VCF file seems intact so... i can't figure it out by myself
what can i do?
thanks in advance
Reg: Absence of length in certain variation events
Hi!
I was annotating the SV calls from Parliament2 when I realized that the Insertion events have 0 length in the tabulated output. Is there a way that we can add the Average length from the SV VCF?
Here is a minimal example
- VCF:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT T8B
chr1 150880 DEL0011SUR N <DEL> 6 PASS SUPP=1;SUPP_VEC=00001;AVGLEN=66;SVTYPE=DEL;SVMETHOD=SURVIVORv2;CHR2=chr1;END=150946;CIPOS=0,0;CIEND=0,0;STRANDS=+-;CALLERS=MANTA GT:SP 0/1:MANTA
chr1 295428 TRA00406SUR N N[chr19:295428[> . PASS SUPP=1;SUPP_VEC=00001;AVGLEN=100000;SVTYPE=BND;SVMETHOD=SURVIVORv2;CHR2=chr19;END=295428;CIPOS=0,0;CIEND=0,0;STRANDS=++;CALLERS=MANTAGT:SP 0/1:MANTA
chr1 341697 INS0013SUR N <INS> . PASS SUPP=1;SUPP_VEC=00001;AVGLEN=59;SVTYPE=INS;SVMETHOD=SURVIVORv2;CHR2=chr1;END=341697;CIPOS=0,0;CIEND=0,0;STRANDS=+-;CALLERS=MANTA GT:SP 1/1:MANTA
chr1 341785 TRA0014SUR N N[chr7:72261928[> . PASS SUPP=1;SUPP_VEC=00001;AVGLEN=100000;SVTYPE=BND;SVMETHOD=SURVIVORv2;CHR2=chr7;END=72261928;CIPOS=0,0;CIEND=0,0;STRANDS=++;CALLERS=MANTAGT:SP 0/1:MANTA
chr1 380129 DEL0015SUR N <DEL> 6 PASS SUPP=4;SUPP_VEC=10111;AVGLEN=6001;SVTYPE=DEL;SVMETHOD=SURVIVORv2;CHR2=chr1;END=386165;CIPOS=-11,116;CIEND=-12,0;STRANDS=+-;CALLERS=BREAKDANCER,DELLY,LUMPY,MANTA GT:SP 1/1:BREAKDANCER,DELLY,LUMPY,MANTA
- SANSA output:
[1]ANNOID query.chr query.start query.chr2 query.end query.id query.qual query.svtype query.ct query.svlen query.startfeature query.endfeature query.containedfeature Gene Fusion
id000000004 chr1 150880 chr1 150946 DEL0011SUR 6 DEL 3to5 66 NA NA NA False
id000000005 chr1 295428 chr19 295428 TRA00406SUR 0 BND 3to3 0 NA NA NA False
id000000006 chr1 341697 chr1 341697 INS0013SUR 0 INS NtoN 0 NA NA NA False
id000000007 chr1 341785 chr7 72261928 TRA0014SUR 0 BND 3to3 0 NA NA NA False
id000000008 chr1 380129 chr1 386165 DEL0015SUR 6 DEL 3to5 6036 LOC100685782(0;-) LOC100685782(0;-) NA False
The last column is just my label to see if genes are fusing or not, so that can be ignored.
Would it be possible to add this average length of insertion to the SANSA annotation?
The representation method of break point pos
I used delly and sansa to build a structural variation analysis pipeline and attempted to evaluate its accuracy through NCCL validation data.
Delly detected the expected mutation. But I'm a bit surprised why there is a 1 bp difference in the representation of breakpoints.
answer:
the sansa result:
| [1]ANNOID | query.chr | query.start | query.chr2 | query.end | query.id | query.qual | query.svtype | query.ct | query.svlen | query.startfeature | query.endfeature |
|---|---|---|---|---|---|---|---|---|---|---|---|
| None | 7 | 55266405 | 7 | 92462404 | INV00002766 | 7260 | INV | 3to3 | 37195999 | EGFR(0;+) | CDK6(0;-) |
| None | 22 | 23632600 | 9 | 133729450 | BND00012515 | 10000 | BND | 5to3 | 0 | BCR(0;+) | ABL1(0;+) |
in delly.bcf
22 23632600 BND00012515 A ]9:133729450]A 10000 PASS PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv1.1.6;END=23632601;CHR2=9;POS2=133729450;PE=431;MAPQ=60;CT=5to3;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=56;SRQ=1;CONSENSUS=AGAATAAAACTAATTTTTTCTCCCAATTTTCTCTTCCTTTTTCTTTTTTCTGTTCCCCCCTTTCTCTTCCAGAGTAAGTACTGGTTTGGGGAGGAGGGTTGCAGCGGCCGAGCCAGGGTCTCCACCCAGGAAGGACTCATCGGGCAGGGTGTGGGGAA;CE=1.97658;RDRATIO=1;SOMATIC GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-253.075,0,-455.964:10000:PASS:222980:329282:106302:2:748:431:155:95 0/0:0,-75.2007,-857.843:10000:PASS:221127:323350:102223:2:1302:0:250:0
7 55266405 INV00002766 C <INV> 7260 PASS PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv1.1.6;END=92462404;PE=101;MAPQ=60;CT=3to3;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=60;INSLEN=0;HOMLEN=1;SR=20;SRQ=1;CONSENSUS=TAATGATGACTAAAGCAAGGGATTGTGATTGTTCATTCATGATCCCACTGCCTTCTTTTCTTGCTTCATCCTCGTGAGCCAGGGAGCTGCGCCCTCGCCATCTGGGGCCTCGCGCGCG;CE=1.97084;RDRATIO=0.997411;SOMATIC GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-193.272,0,-528.756:10000:PASS:197626:345940:220737:2:577:101:173:77 0/0:0,-75.2167,-873.159:10000:PASS:197576:346736:220664:2:768:0:250:0
example the INV00002766，On the IGV image, it can be seen that soft splicing occurs on chromosome 7
between 55266405 and 55266406；
between 92462404 and 92462405
Perhaps it should be said that this is just a small descriptive questions of delly?I am quite concerned about whether there is a conversion between 1base and 0base?I understand that when annotating snv/indel, there is a requirement to annotate according to the 3 'rule of the transcript,Is there a similar requirement in structural variation?
This BND00012515 is particularly confusing for me, as the breakpoint seems to be "chr22 between 23632659-23632661" and "chr9 between 133729450-133729452",Why choose the current breakpoint?
Output location and output format
Hi,
Is it feasible to use delly sansa to specify the output location and format?
I was getting the output bcf file at the current directory and ideally, I would like to get a tab-delimited table to examine fusion candidates like the one in the README.md.
The command I used is below:
Thanks,
Jeff
About the SV Result
Dear Sansa team:
Good morning,
When I ran the sansa for annotation, here showed a message as below:
[W::vcf_parse_info] INFO/END=3751954 is smaller than POS at Pmu2_1:19179541
And the some deletion showed very weird result, the deletion sequence is almost 50% chromosome.
Is there any connection in the warning message and the result??
Thank you very much.
Best
Clarence
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