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Difference between | and || in filtering expressions by bcftools

Hello all,

bcftools have these logical operators that can be used in filtering expressions:

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

What's the difference between || and |? Can someone provide an example and/or usecase for clarification?

The manual have this example:

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

But this is not clear to me.

fin swimmer

bcftools vcf
• 6,273 views • link
written by finswimmer finswimmer

sounds like the the single | works like the linux pipe symbol in a cmdline and the double || as the 'or operator'

• 0 views • link
written by lieven.sterck lieven.sterck

Hm, if it would work like linux pipe where is the difference to &&?

I guess I also have a problem with the description "selects only/all samples". Normaly I select a whole vcf line and not just a sample. Which subcommand of bcftools is able to select specific samples based on expression?

Furthermore the man page said && (same as &), but in the examples this seems to be not the same:

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

I'm confused. The only thing that seems to be clear to me, is that | vs. || or & vs && makes differences in multisample vcf's.

fin swimmer

• 0 views • link
written by finswimmer finswimmer

Hm, looks quite good. But I'm still not sure.

I decided to crosspost directly on bcftools github.

Let's wait and see.

• 1 views • link
written by finswimmer finswimmer

1 answer

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

EDIT: (inserted by a mod)

Answer given on github:

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 .
• 1 views • link
updated by finswimmer finswimmer • written by pd3 • pd3

Hello pd3,

thank you for your response. Unfortunately this isn't an answer to my initial question about the differences between | and ||.

As I wrote a little bit later the difference between & and && is clearly explained in the manual, even if the description "&& (same as &)" is a bit misleading.

But you showed me a use case about selected samples and not only variants. Have to think more about it. But I guess somewhere there is the answer ... :)

fin swimmer

• 1 views • link
written by finswimmer finswimmer

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