How to filter variants called within n base pairs of each other
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2.5 years ago
phongphak.06 ▴ 10

I've filtered variants based on quality and depth using bcftools, but I also want to filter them that were called within 5 base pairs of each other. Is there any tools that can do this?

Example

Before filter:

1 153489 A T 
1 154895 C T
1 154898 G C
1 157355 C A

After filter:

1 153489 A T 
1 157355 C A
vcf SNP sequencing next-gen • 545 views
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2.5 years ago

using vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html

$ java -jar dist/vcffilterjdk.jar --body -e 'String prev_contig=null;int prev_end=-1; public Object apply(final VariantContext vc) {boolean ret=!(vc.getContig().equals(prev_contig)  && vc.getStart() - prev_end <=5); prev_contig=vc.getContig();prev_end=vc.getEnd();return ret; }'  in.vcf
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Thank you so much, I'll try this :)

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