Hi,
My VCF file is annotated with g1k frequency WHEN such a frequency is available.
I want to select all rare variants (with a frequency below a certain cutoff say 1%). Thus I want all lines where this condition is satisfied BUT I also need all the lines where there is no frequency annotation as these are also potential rare variants.
Does anyone know how to do this with bcftools expressions? I have tried but it would seem like bcftools does not provide a way of testing whether a tag is present in the INFO field.
Tim
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written
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tzhughes •
3 answers
Did you try a filter expression?
1 (or 0) to test the presence (or absence) of a flag
FlagA=1 && FlagB=0
associated to an OR expression:
logical operators
&& (same as &), ||, |
associated to a comparison operator?
== (same as =), >, >=, <=, <, !=
should be something like (not tested)
MYFLAG=0 || MYFLAG<0.1
EDIT: with vcffilterjs
cat your.vcf | java -jar dist/vcffilterjs.jar -e '(!variant.hasAttribute("ATT") || variant.getAttributeAsDouble("ATT",999) < 0.2 )'
I got the answer from Petr on the samtools list:
The -i and -e options are complementary and choosing one or the other allows you to include / exclude records without the tag. In your case, this should work:
bcftools view -e'AF>0.99'
I found out that you cannot use -i and -e in the same call to bcftools, but you can use one of them in the first call and pipe the result to a second call to bcftools where you use the second one.
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written
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tzhughes •
bcftools view -i "FREQUENCYTAG<='cutoffvaue' || FREQUENCYTAG='' "
leaving this here for future readers
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written
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Sander G •
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I tried this and it does not work.
I think this syntax
can only be used for tags that are true flags ie that do not have a value. Such tags are defined in the header with Number=0 (number of values) to indicate that they do not have a value. In my case when the frequency is available it is a tag with a value, and when it is not available nothing appears.
I suppose in a way the frequency tag is being used partly as a true flag and partly not. Not my design, but the way it is implemented by several pieces of software.
Tim
I see. in the end, I would use my tool based on javascript: https://github.com/lindenb/jvarkit/wiki/VCFFilterJS see below.