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Question: Filtering no-calls from VCF file
0
gravatar for SOHAIL
4.3 years ago by
SOHAIL • 330
Beijing Institute of Genomics, CAS.
SOHAIL • 330 wrote:

Hi Everyone, i want to remove all sites with more than 5% of no-call (./.) among all the samples in my VCF file, could you please guide me how i can do that variant filtration??

Thanks!

vcf-tools ngs • 2.0k views
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modified 4.3 years ago by Pierre Lindenbaum ♦ 133k • written 4.3 years ago by SOHAIL • 330
1
gravatar for Pierre Lindenbaum
4.3 years ago by
Pierre Lindenbaum ♦ 133k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 133k wrote:

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

 java -jar dist/vcffilterjs.jar -e 'var n=0.0;for(var i=0;i< variant.getNSamples();i++ ) { if(variant.getGenotype(i).isNoCall()) n++;} n/ variant.getNSamples() < 0.05'  input.vcf
ADD COMMENT • link written 4.3 years ago by Pierre Lindenbaum ♦ 133k

Thanks @Pierre.. That worked perfectly fine for me..

However i am curious and interested to use VCFFILTERJS more, Could you please indicate any guideline for writing java scripts expressions particularly for VCFFILTER -e. I have seen some examples but i wanna know about basic functions like: variant.getNSamples() or variant.getGenotype().isNoCall() , etc.

ADD REPLY • link modified 4.3 years ago • written 4.3 years ago by SOHAIL • 330
1

this tools uses a javascript engine (nashorn) that can read the underlying java classes of the htsjdk library like https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/variantcontext/VariantContext.html . It uses a old and well-known java technology called reflection: https://docs.oracle.com/javase/tutorial/reflect/ .

ADD REPLY • link written 4.3 years ago by Pierre Lindenbaum ♦ 133k
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