bcftools "--filter-logic" flag, what + means?

Question

[Eugene A]

Hi,

There is a flag in bcftools, which takes care of FILTER field during merge of several vcf files:

-F, --filter-logic x|+ Set the output record to PASS if any of the inputs is PASS (x), or apply all filters (+), which is the default.

frankly I cant get my head around what does "apply all filters" means here. Help is appreciated!

Best, Eugene

Answer 1

[Pierre Lindenbaum]

When you merge 3 records, if one has filter PASS and other has filter FOO, and the third has filter BAR setting --filter-logic x will return you a record with filter PASS, while --filter-logic + would return you a record with filter FOO,BAR

[Eugene A]

Thanks a lot for the explanation!

Answer 2

[raphael.B]

When you merge 3 records, if one has filter PASS, another has filter FOO, and last as filter 'BAR', setting --filter-logic x will return you a record with filter PASS, while --filter-logic x would return you a record with filter FOO,BAR

[Ram]

PASS + filter_name is filter_name, not PASS,filter_name. PASS means the locus hit no filter. You'll never see a PASS,<something>. Please fix that to make this an accurate answer.