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walaj / svaba

Structural variation and indel detection by local assembly
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Unexpected SV with a zero coordinate #134

Open gudeqing opened 9 months ago

gudeqing commented 9 months ago

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 commented 7 months ago

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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