Filter SNP's for no more than 3 mismatches per 10 bp window

Question

[shubhra.bhattacharya]

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.

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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.

Answer 1

[Pierre Lindenbaum]

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.

[shubhra.bhattacharya]

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.

[Pierre Lindenbaum]

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

make variantsinwindow