Filter variants by specific base change pattern
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4.3 years ago

I would like to filter a VCF file by specific base change e.g. C>T & G>A. It seems that VCFtools does not allow this kind of filter. Does anyone has any idea?

Thanks heaps

SNP • 1.0k views
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4.3 years ago

using VCFfilterJs: https://github.com/lindenb/jvarkit/wiki/VCFFilterJS

java -jar dist/vcffilterjs.jar  -e 'variant.getReference().getDisplayString().equals("A") && variant.getAlternateAlleles().size()==1 && variant.getAlternateAlleles().get(0).getDisplayString().equals("C")' input.vcf

or just awk:

awk -F '\t' '($0 ~/^#/ || ($4=="A" && $5=="C"))' input.vcf
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Is there is a documentation for the functions used in the filtering variant.getReference().getDisplayString() Or how to decide which argument (function/s) to pass to -e

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