I have a question about VCFtools --exclude-bed. I have a bed file that contains <chrom> <start> and <stop> coordinates. However I want to filter my VCF files to only contain those coordinates in the bed file I have made. I know I have to use --exclude-bed however online it is mentioned constantly that --exclude-bed is used to both include and exclude. For example:
--exclude-bed <filename> Include or exclude a set of sites on the basis of a BED file. Only the first three columns (chrom, chromStart and chromEnd) are required. The BED file is expected to have a header line. A site will be kept or excluded if any part of any allele (REF or ALT) at a site is within the range of one of the BED entries.
I only want to make sure that I'm keeping the coordinates in the bed file in my new VCF file. Do I use --exclude-bed? When I try --include-bed as a flag it does not work.
vcftools --vcf $Files/PT_sanger2yTCA454RNvsB73_with_read_groups_filtered_refina2_snps.ann.gatk.vcf --out $Files_made/VCF_intervals_with_transcripts.vcf --exclude-bed $Files_made/VCF_intervals.bed