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Extract gene names from annotated vcf file

I have an annotated vcf file. I want to extract the gene name for each variant. How can I do this? This is the field I am interested in : 

ANN=T|intron_variant|MODIFIER|Plekhg1|ENSMUSG00000040624|transcript|ENSMUST00000120274|protein_coding
|1/16|c.-169+10295G>T||||||,T|intron_variant|MODIFIER**|Plekhg1**|ENSMUSG00000040624|transcript|ENSMUST00000144543|retained_intron| 
 1/7|n.163+10295G>T||||||,T|
intron_variant|MODIFIER|Plekhg1|ENSMUSG00000040624|transcript|ENSMUST00000137111|retained_intron|1/7|n.343+9828G>T||||||"

I want to extract "Plekhg1" from the above entry.

sequencing next-gen
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updated by bioguy24 bioguy24 • written by Gene_MMP8 Gene_MMP8

I formatted the line to better visualize it I am not sure if all of that is supposed to be on a single line.

Is the gene name always in the 4th field (separator |)?

• 0 views • link
written by GenoMax GenoMax

3 answers

How have you got this annotation ?

Is this done generated using SNPeff ? If so, you can extract gene names using snpsift

java -jar SnpSift.jar extractFields file.vcf CHROM POS REF ALT "ANN[*].GENE:"
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written by NB NB

Thanks for answering. Yeah it was generated using SNPEFF. But I don't seem to understand the output of your command. It's giving me the entire vcf file as output. Can I get just the list of genes?

• 0 views • link
written by Gene_MMP8 Gene_MMP8

Please read the documentation of snpsift to understand usage of the commands

Not sure if this would work but you can try try:

java -jar SnpSift.jar extractFields file.vcf  "ANN[*].GENE:"
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written by NB NB

Hi,

Was there an answer to this because I am too having the same issues "ANN[*].GENE:" is just outputting all the ANN fields and not the gene name specifically.

Thanks, Anj

• 1 views • link
written by anjeetjhutty • anjeetjhutty

Try "ANN[*].GENE". This worked for both GENE and GENEID on my vcf.

• 1 views • link
written by tmajaria • tmajaria

What if I want only a list of all unique genes?

• 0 views • link
written by atheeth14 • atheeth14

Usually, the fouth will be gene symbol, they this one:

java -jar SnpSift.jar extractFields file.vcf  "ANN[*].GENE:" | awk -F"|" '{print $4}'

The best choice will be 

java -jar SnpSift.jar extractFields file.vcf CHROM POS REF ALT "ANN[*].GENE:" | awk -F'[\t|]' '{print $1,$2,$3,$4,$8}' OFS="\t"
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written by Shicheng Guo Shicheng Guo

I have not used SNPeff, but if the gene name is always in the fourth field seperated by |

awk -F'|' '{print $4}'
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written by bioguy24 bioguy24

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