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

Variant filter representation #194

Closed
nealsid opened this Issue Mar 28, 2014 · 4 comments

Comments

Projects
4 participants
@nealsid
Contributor

nealsid commented Mar 28, 2014

VCF format specifies that the FILT column can take on the following values:

"PASS" - variant passed all filters
Comma-separated list of failing filters - filters that the variant call failed
"." - no filter applied

(see http://gatkforums.broadinstitute.org/discussion/3401/filter-column-in-vcf-file-from-haplotypecaller for a discussion on the output of the haplotype caller)

Right now, we have two fields in VariantCallingAnnotations:

boolean variantIsPassing
array<string> variantFilters

This table indicates the value of each variable for the different scenarios:

Scenario variantIsPassing variantFilters
Variant Passed true empty
Variant failed filter false failing filter list
No filters applied true empty

@mlinderm brought up that there is some ambiguity - we don't know the difference between variant passing and no filters applied without checking another field (the list of filters applied), and also people doing analysis were only likely to check the boolean, since that's what is done with the VCF field. The proposal is to go back to the original way, which was:

union { null, boolean }  variantIsFiltered = null;
array<string> failingFilters = null;

New table:

Scenario variantIsFiltered failingFilters
Variant Passed false empty
Variant failed filter true failing filter list
No filters applied null empty

Note that in the case where the variant passed, the passing filters should still be available from the VCF header.

Thoughts?

@tdanford tdanford added the discussion label Jun 10, 2014

@tdanford

This comment has been minimized.

Show comment
Hide comment
@tdanford

tdanford Jun 10, 2014

Contributor

Neal, I presume you're still waiting for comments on this one?

Contributor

tdanford commented Jun 10, 2014

Neal, I presume you're still waiting for comments on this one?

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Oct 7, 2015

Member

See also:
Adding quality, filtersFailed, and filtersPassed to Variant ga4gh/ga4gh-schemas#304

Member

heuermh commented Oct 7, 2015

See also:
Adding quality, filtersFailed, and filtersPassed to Variant ga4gh/ga4gh-schemas#304

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jul 6, 2016

Member

Shall we close this?

Member

fnothaft commented Jul 6, 2016

Shall we close this?

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Nov 15, 2016

Member

Fixed by #1250

Member

heuermh commented Nov 15, 2016

Fixed by #1250

@heuermh heuermh closed this Nov 15, 2016

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment