not a known SV format

[genegogo2019]

format is wrong!

[genegogo2019]

I had checked my input VCF format (edited and integrated), it is the same as the original VCFs. However, i still met the problem.

log file: ############################################################################ No SV to annotate in the SVinputFile - Exit without error. ############################################################################

unannotated tsv file: 1_ 15985731: not a known SV format 1 1599072ALU1: not a known SV format 1 70781881: not a known SV format 1 7078188_7078204_INS:ME:ALU1: not a known SV format 1 8277046ALU1: not a known SV format 1 82770511: not a known SV format 1 8446627_1: not a known SV format 1_ 8446627_8446635_INS:ME:ALU1: not a known SV format 1 8446628_1: not a known SV format 1_ 8446635ALU1: not a known SV format 1 12737561_12737575_INS:ME:ALU_1: not a known SV format

[genegogo2019]

Dear author:

This time, the log file wrote No SV to annotate, and the unannotated tsv wasn't written.

Could you tell me which part I have to check?

Thanks

---

log file

AnnotSV 3.0.9

Copyright (C) 2017-2021 GEOFFROY Veronique

Please feel free to contact me for any suggestions or bug reports email: veronique.geoffroy@inserm.fr

Tcl/Tk version: 8.5

Application name used (defined with the "ANNOTSV" environment variable): /opt/ohpc/Taiwania3/pkg/biology/AnnotSV/AnnotSV_v3.0.9

...downloading the configuration data (January 01 2023 - 23:58) ...configuration data by default ...configuration data from /opt/ohpc/Taiwania3/pkg/biology/AnnotSV/AnnotSV_v3.0.9/etc/AnnotSV/configfile ...configuration data given in arguments ...checking all these configuration data

############################################################################ No SV to annotate in the SVinputFile - Exit without error. ############################################################################

－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－ Below is my VCF input files －－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

FORMAT=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TAAD0007-LCL6989_combined

chr1 1598573 INS:ME C 60.636791229248 PASS MEINFO=chr1:1598573_ALU_Plus,1598573,1598574,+;caller=scramble . . chr1 1599072 . g . ac0 TSD=null;ASSESS=1;INTERNAL=NM_001110781,INTRONIC;SVTYPE=ALU;SVLEN=278;MEINFO=AluY,2,280,+;DIFF=0:g9a,c10t,t17a,c48t,g58a,g65a;LP=2;RP=4;RA=-1;PRIOR=false;SR=0;caller=melt GT:GL:DP:AD 0/0:-0,-12.04,-233.9:20:0 chr1 7078188 INS:ME T 105.503662109375 PASS MEINFO=chr1:7078188_ALU_Minus,7078188,7078189,-;caller=scramble . . chr1 7078188 . a . PASS SVTYPE=INS:ME:ALU;SVLEN=84;END=7078204;TSD=+aatGCCAGGGCTTTTT;TSDLEN=16;SUBTYPE=one_half_side_tprt_both;TD_SRC=not_transduction;STRAND=-;AF=0.4482758620689655;LCLIP=11;RCLIP=3;LDISC=7;RDISC=1;LPOLYA=0;RPOLYA=3;LRAWCLIP=13;RRAWCLIP=5;AF_CLIP=13;AF_FMAP=16;AF_DISC=27;AF_CONCORDNT=54;LDRC=0;LDNRC=7;RDRC=0;RDNRC=1;LCOV=40.065;RCOV=40.46;LD_AKR_RC=0;LD_AKR_NRC=7;RD_AKR_RC=1;RD_AKR_NRC=0;LC_CLUSTER=169:190;RC_CLUSTER=251:253;LD_CLUSTER=130.0:252.0;RD_CLUSTER=-1:-1;NINDEL=0;CLIP_LEN=32:49:46:49:8:35:35:35:4:53:49:49:49;INS_INV=Not-5prime-inversion;REF_REP=not_in_Alu_copy;GENE_INFO=intron:ENSG00000171735.19_4:CAMTA1;caller=xtea GT 0/1 chr1 8277046 . C . lc TSD=null;ASSESS=3;INTERNAL=null,null;SVTYPE=ALU;SVLEN=259;MEINFO=AluJo,21,280,+;DIFF=0.21:g204a,t213a,c215g,c220t,t231c,a232g,g270a;LP=5;RP=8;RA=-0.678;PRIOR=false;SR=2;caller=melt GT:GL:DP:AD 0/1:-54,-8.43,-105.6:14:5 chr1 8277051 . . . PASS IMPRECISE;SAMPS=TAAD0007-LCL6989_combined:6;CIPOS=8277045,8277055;SUP=4,2,0,0;POLYA=0;TSD=unknown;CLLEN=267,210;ORIGIN=0,6,0;CLIPPED=-1,-1,-1,-1,-1.00,-1.00;caller=mobster . . chr1 8446627 INS:ME A 163.561294555664 PASS MEINFO=chr1:8446627_ALU_Minus,8446627,8446628,-;caller=scramble . .

[lgmgeo]

Hi @genegogo2019,

My first thought is that your VCF is from Scramble, right? Unfortunately, this tool does not output GT in the format column and the authors have so far not answered the following request: https://github.com/GeneDx/scramble/issues/20

For each SV of an input VCF file, without GT, AnnotSV considers this SV absent from the sample.

So, to annotate your VCF with AnnotSV, you either need to reformat that VCF and add the GT information, or need to create a bed file (without the GT feature).

Best, Véronique

[genegogo2019]

Véronique However, I succeeded to annotate VCF output files from scramble alone.

With best wishes, 段德敏(Demin-Duan)

[genegogo2019]

Dear author: I succeeded annotation on Scramble alone, but failed while I merge with other MEI callers output file. The attached file is annotated file for scramble output.

With best wishes, 段德敏

[lgmgeo]

Not sure to understand your need. AnnotSV is not a tool dedicated to merge VCF.

[genegogo2019]

Okay, I am not merging the VCF files with AnnotSV. I merged the VCFs from different callers and filtered and then threw into the AnnotSV. May be I will find a solution. Thanks for your kindly reply.

With best wishes, 段德敏

[lgmgeo]

To merge SV VCF, I can advise you truvari or jasmine .

[genegogo2019]

Dear author: I solved the problem. It was my fault that extra space before the fields. I could annotate successfully. Thanks.