I have a list of genes. and i want to extract the snps and indels from my VCF file (that i generated using GATK pipeline ) from  genes coordinates on . The list of genes coordinates:

    Gene Name   Accession_no.   Start_Position   End_Position   Strand 
    Rv0194         NC_000962.3       226878	        230462            + 

 
I was looking bedtools but it is asking for .bed format of genes nd as well .bed of bam files. how to do it ? or any other options/tools/scripts?

Like i tried tabix:

    bgzip ERR038736_UnifiedGenotyper_variants_raw_snp.vcf
    tabix ERR038736_UnifiedGenotyper_variants_raw_snp.vcf.gz
    tabix ERR038736_UnifiedGenotyper_variants_raw_snp.vcf.gz AL123456.3:226878-230462 > Rv0194

and this gave me the variants like this:

    AL123456.3      227098  .       T       C       6730.77 .       AC=2;AF=1.00;AN=2;DP=172;Dels=0.
    AL123456.3      228069  .       G       A       7132.77 .       AC=2;AF=1.00;AN=2;BaseQRankSum=-
    AL123456.3      228168  .       G       C       6682.77 .       AC=2;AF=1.00;AN=2;DP=171;Dels=0.

But this is not a vcf file and i can only extract it one at a time. I want to extract all variants against a list of coordinates and store it in a vcf output. 

Can anyone help me it this?

BEDOPS:

    $ vcf2bed --insertions < snps.vcf > insertions.bed
    $ vcf2bed --deletions < snps.vcf > deletions.bed
    $ vcf2bed --snvs < snps.vcf > snvs.bed

https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html