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  • vcftools to update vcf with gene info from bed

    I am trying to add gene information to a vcf file using vcftools:

    Code:
    vcftools annotate \
      -a genes.bed.gz \
      -c CHROM,FROM,TO,GENE \
      -h <(echo '##INFO=<ID=GENE,Number=1,Type=String,Description="Gene name">') \
      TSVC_001.vcf.gz
    genes.bed.gz is compressed using bzip, sorted, and indexed by tabix
    Code:
    for f in /home/cmccabe/Desktop/tabix/*.bed ; do
        bname=$(basename $f)
        vcf-sort $f | bgzip -c > $f.gz ; tabix -p bed $f.gz
    done
    genes.bed.gz
    Code:
    chr1	955543	955763	AGRN
    chr1	957571	957852	AGRN
    chr1	970621	970740	AGRN

    The vcftools command runs but I do not see that the vcf.gz was updated with the gene information from the bed file. Thank you .
    Last edited by cmccabe; 02-24-2016, 12:28 PM. Reason: fixed format

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