Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

why SVSIZE=number+ #139

Open
jingydz opened this issue Oct 24, 2023 · 2 comments
Open

why SVSIZE=number+ #139

jingydz opened this issue Oct 24, 2023 · 2 comments

Comments

@jingydz
Copy link

jingydz commented Oct 24, 2023

Hi, why some records are "+"
for example:
chr1 1391725 chr1:1391725:FG N INS:SVSIZE=368+:AGGREGATED 162 PASS ABHet=0.5;ABHom=1;AC=1;AF=0.0001139;AN=8776;END=1391725;LEFT_SVINSSEQ=AAAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAAAATTAGCCGGGCGAGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCCAGGGGGCGGAGCCTGCAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGCGAGACTCCGTCTCAAAAAAAA;MaxAAS=9;MaxAASR=0.5;MaxAltPP=9;NHet=1;NHomAlt=0;NHomRef=4387;NUM_MERGED_SVS=1;PASS_AC=1;PASS_AN=8774;PASS_ratio=0.9998;QD=16.2;RELATED_SV_ID=209;RIGHT_SVINSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA;RefLen=1;SVMODEL=AGGREGATED;SVTYPE=INS;SV_ID=208;SeqDepth=158115;VarType=FG GT:FT:AD:MD:DP:RA:PP:GQ:PL 0/0:PASS:54,0:1:55:55,1:0:99:0,150,255

@jingydz
Copy link
Author

jingydz commented Oct 24, 2023

The length of "left + right" sequence is the 368, why there is a plus flag in the end?
Can I ignore the plus flag?

@hannespetur
Copy link
Member

Hey. SVSIZE=number+ is used if the full size of the insertion is not known (only the sizes of the breakpoint sequences).

Best,
Hannes

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants