filtering vcfs by at least lof variants

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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written 5.2 years ago by storm1907 •

snpSift is the tool used for filtering, not snpEff https://pcingola.github.io/SnpEff/ss_introduction/

snpSift doesn't use the INFO/CSQ tag but the INFO/ANN tag. https://pcingola.github.io/SnpEff/se_inputoutput/#ann-field-vcf-output-files

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written 5.2 years ago by Pierre Lindenbaum

1 answer

The -lof flag (without anything after it) will add the LOF tag to the INFO field in the VCF file. It should look something like this for the GRCm38.99 database (adjust this to your reference genome):

java -Xmx4g -jar snpEff.jar -lof GRCm38.99 yourFile.vcf.gz > yourFile.eff.vcf

After that you can filter using BCFtools or SnpSift depending on your needs. Examples here: how to extract gene name for LOF (loss of function) variants

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written 5.2 years ago by atorreso •

OK, I tried with hg38.fasta after -lof, but got 
java.lang.RuntimeException: Property: 'hg38.fasta.genome' not found
        at org.snpeff.interval.Genome.<init>(Genome.java:104)
        at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:693)
        at org.snpeff.snpEffect.Config.readConfig(Config.java:661)
        at org.snpeff.snpEffect.Config.init(Config.java:487)
        at org.snpeff.snpEffect.Config.<init>(Config.java:121)
        at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
        at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:939)
        at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:923)
        at org.snpeff.SnpEff.run(SnpEff.java:1188)

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written 5.2 years ago by storm1907 •

snpEff requires a database. I recommend reading their manual first: https://pcingola.github.io/SnpEff/se_introduction/

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written 5.2 years ago by atorreso •

This is the output after java -jar /mnt/home/tools/snpEff/snpEff.jar -lof GRCh38.99 $file > $outfile

Does not look like any tag is added

 chrX    155491696       .       G       C       52.8    PASS    CSQ=|FAIL|0.00|0.03|0.00|0.00|42|-30|-30|-25|||MODIFIER|TMLHE|ENSG00000185973|ENST00000334398|protein_coding||7/7|||||,|FAIL|0.00|0.03|0.00|0.00|42|-30|-30|-25|||MODIFIER|TMLHE-AS1|ENSG00000224533|ENST00000433624|lncRNA||3/3|||||;ANN=C|downstream_gene_variant|MODIFIER|BX571846.1|ENSG00000225393|transcript|ENST00000447347.1|pseudogene||n.*4650G>C|||||4650|,C|downstream_gene_variant|MODIFIER|TMLHE|ENSG00000185973|transcript|ENST00000369439.4|protein_coding||c.*869C>G|||||839|,C|intron_variant|MODIFIER|TMLHE-AS1|ENSG00000224533|transcript|ENST00000433624.1|pseudogene|3/3|n.472-1184G>C||||||,C|intron_variant|MODIFIER|TMLHE|ENSG00000185973|transcript|ENST00000334398.8|protein_coding|7/7|c.1135-30C>G||||||,C|intron_variant|MODIFIER|TMLHE|ENSG00000185973|transcript|ENST00000449645.2|processed_transcript|1/1|n.209-30C>G||||||,C|intron_variant|MODIFIER|TMLHE-AS1|ENSG00000224533|transcript|ENST00000452506.1|pseudogene|1/1|n.67+2307G>C||||||    GT:GQ:DP:AD:VAF:PL      1/1:27:12:0,12:1:52,26,0

Are there any other options except snpEff?

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written 5.2 years ago by storm1907 •