Logical operators

[finswimmer]

Hello,

the manual says these logical operators can be used in filtering expressions:

&& (same as &), ||, |

I read it like: "It doesn't matter if one use & or &&."

But in the later examples there seems to be a different behaviour:

FMT/DP>10  & FMT/GQ>10 .. both conditions must be satisfied within one sample
FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples

Furthermore I don't understand the difference between | and ||. Can someone please give me an example and usecase for both to get a better understanding of this?

The manual says something about "select [...] samples". But which bcftools subcommand is able to select samples based on expressions?

I've posted this question yesterday on biostars. But until now there are just a few guesses about the differences. So I decided to ask directly on the source :)

fin swimmer

[pd3]

Say your VCF contains the per-sample depth and genotype quality annotations and you want to include only sites where one or more samples have big enough coverage (DP>10) and genotype quality (GQ>20). The expression -i 'FMT/DP>10 & FMT/GQ>20' selects sites where the conditions are satisfied within the same sample:

$ bcftools query -i'FMT/DP>10 & FMT/GQ>20' -f'%POS[\t%SAMPLE:DP=%DP GQ=%GQ]\n' file.bcf
49979   SampleA:DP=10 GQ=50     SampleB:DP=20 GQ=40

On the other hand, if you need to include sites where both conditions met but not necessarily in the same sample, use the && operator rather than &:

$ bcftools query -i'FMT/DP>10 && FMT/GQ>20' -f'%POS[\t%SAMPLE:DP=%DP GQ=%GQ]\n' file.bcf
31771   SampleA:DP=10 GQ=50     SampleB:DP=40 GQ=20
49979   SampleA:DP=10 GQ=50     SampleB:DP=20 GQ=40

This example is taken from http://samtools.github.io/bcftools/howtos/filtering.html

[finswimmer]

Hello @pd3 ,

I somehow miss the notification about your response here. So please excuse my late response.

As I wrote on biostars unfortunately this is not an answer on the question what's the difference between | and || and when to use what. The example on the manual page is unclear to me.

So please let me aks you to reopen this question.

fin swimmer

[pd3]

Well, sorry to demonstrate the difference on & and && instead of | of ||, but it's the same priniciple.

The manual page says it all:

QUAL>10 |  FMT/GQ>10   .. true for sites with QUAL>10 or a sample with GQ>10, but selects only samples with GQ>10
QUAL>10 || FMT/GQ>10   .. true for sites with QUAL>10 or a sample with GQ>10, plus selects all samples at such sites

Or you can try to run yourself:

$ bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' test/view.filter.vcf 
3162006 A 19

3162007 A .
3162007 B .

$ bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' test/view.filter.vcf 
3162006 A 19
3162006 B 1

3162007 A .
3162007 B .

[finswimmer]

Hey @pd3 ,

thanks for reopening and your additional informations. Your example showed it quite clear.

It would be very good if the manual will be expanded by such a practical example as you show.

Further more the part "&& (same as &)" should be edited, as it is not the same.

fin swimmer

PS: For the sake of completeness I will edit your answer on biostars and copy&paste the answer from here to there.

[pd3]

Thank you. I'll update the documentation as well.