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Annotate genes from gtf file to vcf file

Hi all,

Is there any tool that can help to annotate the genes from GTF file to a (columns) in the vcf file?

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sample1
1       51479   .       T       A       570.64  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.121e+00;DP=25;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.83;ReadPosRankSum=0.953;SOR=0.760    GT:AD:DP:GQ:PL  0/1:5,20:25:99:578,0,99
1       51803   .       T       C       627.06  PASS    AC=2;AF=1.00;AN=2;DP=19;ExcessHet=0.0000;FS=0.000;MLEAC=2;
gtf genomics vcf
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written by QX • QX

Don't forget to follow up on your threads, that is bad etiquette. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

not tested:

gunzip -c  in.gtf.gz |\
awk -F '\t' '($3=="gene") {G="."; N=split($9,a,/[; "]*/); for(i=1;i+1<=N;i++){if(a[i]=="gene_name") {G=a[i+1];break;}} printf("%s\t%d\t%d\t%s\n",$1,int($4)-1,$5,G);}'  |\
sort -t $'\t' -k1,1 -k2,2n |\
bgzip > genes.bed.gz 

tabix -p bed  genes.bed.gz 


echo '##INFO=<ID=GENE,Number=.,Type=String,Description="genes">' > genes.header


bcftools annotate -a "genes.bed.gz " -h  genes.header -c "CHROM,FROM,TO,GENE" --merge-logic 'GENE:unique' in.vcf

or build a SNPEFF database with your gtf and annotate with snpeff https://pcingola.github.io/SnpEff/snpeff/build_db_gff_gtf/

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written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre Lindenbaum,

It works, many thanks!

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written by QX • QX

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