Unexpected SV with a zero coordinate

[gudeqing]

Hi, I am using the latest SvABA(1.1.3) my pipeline, and the tool AnnotSv reported an invalid record from the result of SvABA in all samples:

chrM	0	275359916:1	N	]chrM:16641]N	99	PASS	DISC_MAPQ=50;EVDNC=DSCRD;IMPRECISE;MAPQ=50;MATEID=275359916:2;MATENM=-1;NM=-1;NUMPARTS=0;SCTG=chrM:0(-)-chrM:16641(+)__91_1_16571D;SPAN=16641;SVTYPE=BND	GT:AD:DP:GQ:PL:SR:DR:LR:LO	1/1:89:71:24.9:273.9,24.9,0:0:89:-274:274
chrM	16641	275359916:2	N	N[chrM:0[	99	PASS	DISC_MAPQ=60;EVDNC=DSCRD;IMPRECISE;MAPQ=60;MATEID=275359916:1;MATENM=-1;NM=-1;NUMPARTS=0;SCTG=chrM:0(-)-chrM:16641(+)__91_1_16571D;SPAN=16641;SVTYPE=BND	GT:AD:DP:GQ:PL:SR:DR:LR:LO	1/1:89:71:24.9:273.9,24.9,0:0:89:-274:274

I guess the point is that the coordinate of this SV is zero. In a VCF file, the position of each variant is represented by the POS field, which specifies its location on the reference genome (typically 1-based, meaning counting starts from 1). Therefore, the value of the POS field should be an integer greater than 0. So, what could be the reason of getting the result？

The command is

set -o pipefail
svaba run --threads 8 -a RAJI4 -G /home/hxbio04/hg19/genome.fa -t RAJI4.sorted.bam --max-coverage 50000 --hp

Best wishes!

[walaj]

I don't know! The default constructor for the object that holds the breakpoints has a value of 0, but I don't know why this wouldn't always be set in the pipeline.

On Thu, Feb 22, 2024 at 1:19 AM gudeqing @.***> wrote:

Hi, I am using the latest SvABA(v1.2.0) in my pipeline, and the tool AnnotSv reported an invalid record from the result of SvABA in all samples:

chrM 0 275359916:1 N ]chrM:16641]N 99 PASS DISC_MAPQ=50;EVDNC=DSCRD;IMPRECISE;MAPQ=50;MATEID=275359916:2;MATENM=-1;NM=-1;NUMPARTS=0;SCTG=chrM:0(-)-chrM:16641(+)__91_1_16571D;SPAN=16641;SVTYPE=BND GT:AD:DP:GQ:PL:SR:DR:LR:LO 1/1:89:71:24.9:273.9,24.9,0:0:89:-274:274 chrM 16641 275359916:2 N N[chrM:0[ 99 PASS DISC_MAPQ=60;EVDNC=DSCRD;IMPRECISE;MAPQ=60;MATEID=275359916:1;MATENM=-1;NM=-1;NUMPARTS=0;SCTG=chrM:0(-)-chrM:16641(+)__91_1_16571D;SPAN=16641;SVTYPE=BND GT:AD:DP:GQ:PL:SR:DR:LR:LO 1/1:89:71:24.9:273.9,24.9,0:0:89:-274:274

I guess the point is that the coordinate of this SV is zero. In a VCF file, the position of each variant is represented by the POS field, which specifies its location on the reference genome (typically 1-based, meaning counting starts from 1). Therefore, the value of the POS field should be an integer greater than 0. So, what could be the reason of getting the result？

The command is

set -o pipefail svaba run --threads 8 -a RAJI4 -G /home/hxbio04/hg19/genome.fa -t RAJI4.sorted.bam --max-coverage 50000 --hp

Best wishes!

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