Question: Filter SNP's for no more than 3 mismatches per 10 bp window
0
gravatar for shubhra.bhattacharya
21 months ago by
shubhra.bhattacharya120 wrote:

Hi

The version of my JAVA is: 1.8 The version of my GATK is: 3.7.0 My OS is: Ubuntu 14.04.2 LTS My processor is: Intel Core i5-4440 CPU @ 3.10GHz × 4

I have been successful in creating a vcf file using Unified Genotyper (GATK). This Vcf file was obtained from a merged bam. The merged bam was obtained from 10 different bam files.(10 different samples but of same organism).

I now want to get rid of my false-positives For this I want to get rid of SNP's with *

no more than 3 mismatches per 10 bp window.


I am aware of GATK filtervariants which can do this but due to some unidentified error in GATK its showing impossibly high run time to do so. (1000 weeks!!)

Is there any alternative way by which I can do this? or has anyone faced the same problem with GATK before?

Any help will be highly valued.

gatk snp mismatch filter • 656 views
ADD COMMENTlink modified 21 months ago by Pierre Lindenbaum123k • written 21 months ago by shubhra.bhattacharya120
1
gravatar for Pierre Lindenbaum
21 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

I've written this: http://lindenb.github.io/jvarkit/VariantsInWindow some times ago. It should be fast, but I've not used it much= use with care.

ADD COMMENTlink written 21 months ago by Pierre Lindenbaum123k

Thanks a lot Pierre for your prompt reply.

When I try to make vcfwindowvariants. It gives the error: make: * No rule to make target 'vcfwindowvariants'. Stop.

In the tools directory : /jvarkit/src/main/java/com/github/lindenb/jvarkit/tools I cannot locate vcfwindowvariants.

Please help.

ADD REPLYlink written 21 months ago by shubhra.bhattacharya120
1

you're right ! sorry, the documentation was wrong, I've updated it: https://github.com/lindenb/jvarkit/commit/d93b31743b4eaa7808ca8f02e89174c288c574cd

make variantsinwindow
ADD REPLYlink written 21 months ago by Pierre Lindenbaum123k
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