Variant filter representation

[nealsid]

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]

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

[heuermh]

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

[fnothaft]

Shall we close this?

[heuermh]

Fixed by #1250