intersecting bed and vcf files
Hello,
I want to intersect a vcf file with a bed file for which I use the following command:
intersectBed -a vcf -b bedfile > newvcf
The problem here is that the file newvcf is a vcf file without a header so when I want to intersect the two vcfs with this command, I am not able to do that:
vcf-isec -n +2 A.vcf.gz B.vcf.qz | bgzip -c > out.vcf
How I can create the intersect with bed file so I can have a proper vcf file with header as the output?
Thanks!
1 answer
Log in to answer this question.
More posts like this
-
Using BCFtools to intersect multiple VCF files
written by Hadi M •
-
Bedtools intersect behavior under different coordinate systems?
written by edsouza •
-
Intersection of a BED genes with multiple VCFs: report only if at least N intersection.
written by 乙
-
Merging multiple vcf files into one
written by hpapoli
-
using vcftools to add gene name to vcf file
written by bioguy24
-
How bcftools isec works ?
written by sacha
-
intersecting bed and vcf files for polyploid samples
written by hpapoli
-
BedTools IntersectBed resulting in Segmentation Fault with BedFile
written by ali •
-
Bedtools Compare Multiple Bed Files to one Bed files?
written by BIOTIN •
-
Bedtools Compare Multiple Bed Files?
written by Bioscientist
