Annotate genes from gtf file to vcf file

Question

[QX]

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;

[Pierre Lindenbaum]

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Answer 1

[Pierre Lindenbaum]

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/

[QX]

Hi Pierre Lindenbaum,

It works, many thanks!