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

How to understand the structural variation with bedpe format? #3

Open
Shicheng-Guo opened this issue Nov 19, 2020 · 0 comments
Open

Comments

@Shicheng-Guo
Copy link

Dear Cancer IT group:

I downloaded the Nature Paper and supplementary data from the following website:

https://dcc.icgc.org/releases/PCAWG/consensus_sv

However, I find I am confused about the format and the interpretation. How to understand the structural variation with bedpe format?

For example, the first one is duplication, how to know which region is duplicated ? how many duplicates happened?

What does start1 and end1 mean? why they are always having 1b difference?

chrom1  start1  end1    chrom2  start2  end2    sv_id   pe_support  strand1 strand2 svclass
1   10428600    10428601    1   10582238    10582239    SVMERGE93   80  -   +   DUP
1   26939174    26939175    1   27518317    27518318    SVMERGE102  89  +   -   DEL
1   29834388    29834389    1   33723647    33723648    SVMERGE100  107 -   -   t2tINV
1   29834417    29834418    1   33723675    33723676    SVMERGE101  87  +   +   h2hINV
1   32728334    32728335    1   32845969    32845970    SVMERGE99   33  -   +   DUP
1   78236345    78236346    1   78427706    78427707    SVMERGE98   71  +   -   DEL
1   151858704   151858705   13  44927717    44927718    SVMERGE151  75  -   +   TRA
1   151873175   151873176   1   183511505   183511506   SVMERGE152  41  +   -   DEL
1   151887225   151887226   13  44703672    44703673    SVMERGE163  65  -   -   TRA

Thanks.

Shicheng

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

1 participant