filtering vcfs by at least lof variants

1

Hello,

I have vcf file with following INFO field for each variant. I would like to filter after MAF>30%, protein prediction, and also after LOF variants.

I tried

java -jar /mnt/home//tools/snpEff/snpEff.jar  -lof 

but is not clear, what argument should I put after -lof

chr1    935954  .       G       T       52.6    PASS    CSQ=|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000342066|protein_coding||5/13|||||,|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000616016|protein_coding||5/12|||||,|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000616125|protein_coding||5/11|||||,|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000617307|protein_coding||5/12|||||,|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000618181|protein_coding||4/10|||||,|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000618323|protein_coding||5/11|||||,|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000618779|protein_coding||5/12|||||,|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000620200|protein_coding||4/8|||||,|FAIL|0.00|0.00|0.00|0.00|14|23|43|47|||MODIFIER|SAMD11|ENSG00000187634|ENST00000622503|protein_coding||5/13|||||        GT:GQ:DP:AD:VAF:PL      0/1:53:22:9,13:0.590909:52,0,67 

Can somebody explain that?

Thank you!


lof

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updated 1 hour ago by

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written 2 hours ago by

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