Extract gene names from annotated vcf file

Question

[Gene_MMP8]

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.

[GenoMax]

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 |)?

Answer 1

[NB]

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:"

[Gene_MMP8]

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?

[NB]

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:"

[anjeetjhutty]

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

[tmajaria]

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

[atheeth14]

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

Answer 2

[Shicheng Guo]

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"

Answer 3

[bioguy24]

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

awk -F'|' '{print $4}'