-
Notifications
You must be signed in to change notification settings - Fork 174
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
Acceptable values for confidence interval tags #224
Comments
Technically, the specifications don't place any restrictions other on CIPOS other than they be two number so a confidence interval of
A CIPOS with a (non-zero) positive starting position or a negative ending position doesn't really make sense since the called variant position would be outside the confidence interval. |
This ticket highlights the need for the VCF spec to be more explicit in its definition and treatment of CIPOS and CIEND. In order for values for these fields to make sense (as @d-cameron points out), there is some basic logic that must be followed. That logic should be spelled out in the spec. The following is a proposal ('CI*' means 'CIPOS and/or CIEND'):
Another important aspect of CI* that needs to be explicitly defined in the spec is: What exactly do the values in CI* represent? Are they the boundaries of a statistical 95% confidence interval? Are they "hard boundaries"? See related discussion in #132 . |
I just want to mention that clarifications/modifications to the CIPOS/CIEND and IMPRECISE tags in the spec are being discussed in the conversation going on around #231 that is being moderated by @thefferon . Anyone interested in this issue should probably comment on that PR and/or contact @thefferon to join the detailed discussion around the issues that have been brought up there. |
Closing in favor of #231 |
Given we're reopened this, we should also explicitly state what CIPOS/IMPRECISE and CIPOS/HOMSEQ mean. I/GRIDSS are writing CIPOS/IMPRECISE when there is only RP support and the exact position is known and writing CIPOS/HOMSEQ when the exact breakpoint sequence is know but there is a microhomology at the breakpoint. We should either:
|
I was curious as to what values are acceptable for confidence interval fields like CIPOS in Structural Variants.
The fields involving confidence intervals are : CIPOS, CIEND, CILEN, CICN and CICNADJ
For example, CIEND should contain 2 integers and in the example in the spec, the first value is negative and the second one positive.
So, what range of values is acceptable for these two integers? Can they be
0
too? Also, can they have equal values?The text was updated successfully, but these errors were encountered: