added simple-event-annotation as a command line script

[mnshgl0110]

Created a command line utility for simple-event-annotation that can be run using:

Rscript simple-event-annotation.R <PATH_TO_INPUT_VCF> <GENOME_NAME> <OUTPUT_PREFIX>

This script works directly on the output on GRIDSS and does not require any manual change.

[SunWinner01]

Hello, sorry to bother you. I encountered some issues while running this Rscript. I received the file, but it did not contain the expected columns. May I consult with you? Thank you very much! @mnshgl0110

[papenfuss]

Please send through a snapshot of the output file and any error messages. Kind regards, Tony From: SunWinner01 ***@***.***> Date: Thursday, 10 October 2024 at 2:10 PM To: PapenfussLab/gridss ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [PapenfussLab/gridss] added simple-event-annotation as a command line script (PR #618) Hello, sorry to bother you. I encountered some issues while running this Rscript. I received the file, but it did not contain the expected columns. May I consult with you? Thank you very much! @mnshgl0110<https://github.com/mnshgl0110> — Reply to this email directly, view it on GitHub<#618 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGWMFFCJIXVLWDBXSA6UWDZ2XVYVAVCNFSM6AAAAABPVZL5POVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBTHA2DSMJXGI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[SunWinner01]

Hello, thank you very much for your reply. The situation is as follows.
I have tested one of my .vcf generated by Gridss based on the script and commands you provided, but several warnings have appeared. The warnings are as follows:

Warning: ‘timedatectl’ indicates the non-existent timezone name ‘n/a’
Warning: Your system is mis-configured: ‘/etc/localtime’ is not a symlink
Warning: ‘/etc/localtime’ is not identical to any known timezone file
Warning message:
In .breakpointRanges(x, ...) :
Removing 4 unpaired breakend variants. Use inferMissingBreakends=TRUE to recover with inferred partner breakends. Missing breakends: gridss6ff_68h, gridss24bf_1064o, gridss30bb_198h, gridss53ff_234o

I want to know if this will have a negative impact on my .annotated.vcf? Is this considered normal?
However, despite the presence of warnings, I can still obtain the .annotated.vcf. By annotating on each line of the .vcf, some lines already have the SIMPLE.TYPE, but some lines still do not receive the SIMPLE.TYPE . How should I handle this situation?

NC_047559.1 9671 gridss0b_4b T .GGGTTAGGGT 262.13 LOW_QUAL ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=1X;ASQ=0;ASRP=0;ASSR=0;BA=1;BAQ=98.12;BASRP=2;BASSR=5;BEID=asm0-20871;BEIDH=-1;BEIDL=9;BMQ=30.5;BMQN=21;BMQX=51;BQ=262.13;BSC=7;BSCQ=72.39;BUM=4;BUMQ=91.61;BVF=6;CAS=0;CASQ=0;CQ=206.75;EVENT=gridss0b_4;IC=0;IQ=0;RAS=0;RASQ=0;REF=12;REFPAIR=0;RP=0;RPQ=0;SB=0.33333334;SC=1X;SR=0;SRQ=0;SVTYPE=BND;VF=0 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.333:0:0:0:0:0:0:0:98.12:2:5:262.13:7:72.39:4:91.61:6:0:0:0:0:0:12:0:0:0:0:0:0
NC_047559.1 15934 gridss0f_3b G GTATAGTCTAGGGTATATCCCTGGGTTAAACCCGGGTATATCCTGGGTTTAACCCGGGTATACCCTGAGTTTATCCCGGGTTTAACCCGGGTATACCCTGGGTTTACCCCGGGTATACCCTGGGTTAAACCCGGGTATACCC. 289.37 LOW_QUAL ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=1X;ASQ=0;ASRP=0;ASSR=0;BA=1;BAQ=144.68;BASRP=3;BASSR=6;BEID=asm0-7;BEIDH=-1;BEIDL=0;BMQ=45.4;BMQN=23;BMQX=60;BQ=289.37;BSC=6;BSCQ=70.47;BUM=3;BUMQ=74.22;BVF=6;CAS=0;CASQ=0;CQ=289.37;EVENT=gridss0f_3;IC=0;IQ=0;RAS=0;RASQ=0;REF=113;REFPAIR=0;RP=0;RPQ=0;SB=0.5;SC=1X;SR=0;SRQ=0;SVTYPE=BND;VF=0 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.05:0:0:0:0:0:0:0:144.68:3:6:289.37:6:70.47:3:74.22:6:0:0:0:0:0:113:0:0:0:0:0:0
NC_047559.1 16092 gridss0b_11b G .ATTAACATTATGTTGATGTAAGGAAAGTAACTTCATAAAATATATGTTGATGTCATTTTTGATAAGAGTAAAAAATGAGTATGTTTAACAACAAATATGAAAACTAATAAACGAATGATCTTTAAAATAAATTGTTG 310.09 ASSEMBLY_BIAS;LOW_QUAL;NO_RP;NO_SR ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=1X;ASQ=0;ASRP=0;ASSR=0;BA=1;BAQ=310.09;BASRP=0;BASSR=22;BEID=asm0-20878;BEIDH=-1;BEIDL=136;BMQ=59;BMQN=59;BMQX=59;BQ=310.09;BSC=0;BSCQ=0;BUM=0;BUMQ=0;BVF=16;CAS=0;CASQ=0;CQ=310.09;EVENT=gridss0b_11;IC=0;IQ=0;RAS=0;RASQ=0;REF=132;REFPAIR=1;RP=0;RPQ=0;SB=0.59090906;SC=1X;SR=0;SRQ=0;SVTYPE=BND;VF=0 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.107:0:0:0:0:0:0:0:310.09:0:22:310.09:0:0:0:0:16:0:0:0:0:0:132:1:0:0:0:0:0
NC_047559.1 16238 gridss0f_5b G GTTAGGGTTAGGGTTAGGGTTAGGGTT. 98.9 LOW_QUAL ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=1X;ASQ=0;ASRP=0;ASSR=0;BA=1;BAQ=51.22;BASRP=2;BASSR=0;BEID=asm0-6;BEIDH=-1;BEIDL=137;BMQ=41;BMQN=32;BMQX=60;BQ=98.9;BSC=2;BSCQ=22.07;BUM=1;BUMQ=25.61;BVF=3;CAS=0;CASQ=0;CQ=121.9;EVENT=gridss0f_5;IC=0;IQ=0;RAS=0;RASQ=0;REF=426;REFPAIR=1;RP=0;RPQ=0;SB=0.5833333;SC=1X;SR=0;SRQ=0;SVTYPE=BND;VF=0 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.006977:0:0:0:0:0:0:0:51.22:2:0:98.9:2:22.07:1:25.61:3:0:0:0:0:0:426:1:0:0:0:0:0
NC_047559.1 20255 gridss0fb_8o G G[NC_047559.1:20279[ 54.65 LOW_QUAL;NO_ASSEMBLY ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=1X3N1X;ASQ=0;ASRP=0;ASSR=0;BA=0;BAQ=0;BASRP=0;BASSR=0;BQ=0;BSC=0;BSCQ=0;BUM=0;BUMQ=0;BVF=0;CAS=0;CASQ=0;CIPOS=-2,2;CIRPOS=-2,2;CQ=54.65;EVENT=gridss0fb_8;HOMLEN=4;HOMSEQ=GGGT;IC=2;IHOMPOS=-2,18;IQ=54.65;MATEID=gridss0fb_8h;MQ=33.5;MQN=27;MQX=40;RAS=0;RASQ=0;REF=4;REFPAIR=0;RP=0;RPQ=0;SB=1;SC=81M1X3N1X;SR=0;SRQ=0;SVTYPE=BND;VF=2;SIMPLE_TYPE=DEL;SVLEN=-23 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.333:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:2:54.65:54.65:0:4:0:0:0:0:0:2

In addition, I would like to ask why the GT in the .vcf is always "." and why there is no numerical value?
The above are all my questions. I sincerely hope to receive your reply. Thank you very much! @papenfuss