Unexpected SV with a zero coordinate #134
Description
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!