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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!
The text was updated successfully, but these errors were encountered:
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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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:
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
Best wishes!
The text was updated successfully, but these errors were encountered: