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Question: How to filter variants called within n base pairs of each other
1
gravatar for phongphak.06
2.4 years ago by
phongphak.06 • 10
phongphak.06 • 10 wrote:

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
sequencing snp next-gen vcf • 515 views
ADD COMMENT • link •
modified 2.4 years ago by Pierre Lindenbaum ♦ 134k • written 2.4 years ago by phongphak.06 • 10
0
gravatar for Pierre Lindenbaum
2.4 years ago by
Pierre Lindenbaum ♦ 134k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 134k wrote:

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
ADD COMMENT • link written 2.4 years ago by Pierre Lindenbaum ♦ 134k

Thank you so much, I'll try this :)

ADD REPLY • link written 2.4 years ago by phongphak.06 • 10
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