comparing variants between two VCF files

Question

[BDK_compbio]

I have two VCF files (e.g. SV1.vcf.gz, SV2.vcf.gz) and a bed file (reg.bed). I would like to compare the variants among them in the BED regions. The comparison includes the common variants and unique variants present in SV1 and SV2.

I am currently doing this with several steps like the followings

tabix -R reg.bed SV1.vcf.gz > SV1.BR.vcf.gz  
tabix -R reg.bed SV2.vcf.gz > SV2.BR.vcf.gz

It seems the above two steps do not retain the headers, so I needed to extract the headers and append them at the beginning and then use bgzip and tabix. For finding the common and unique variants among these two, I used the following

bcftools isec -n~11 -c all SV1.BR.vcf.gz SV2.BR.vcf.gz > common.txt
bcftools view -T common.txt SV1.BR.vcf.gz -Oz > SV1.unique.txt
bcftools view -T common.txt SV2.BR.vcf.gz -Oz > SV2.unique.txt 

I am just wondering if there exist any other tools for this without running the script with the above commands. Any tools that also produces some good visualizations will be really useful.

[Jeremy Leipzig]

tabix -h will include the header

Answer 1

[Jeremy Leipzig]

You may want to look at https://github.com/asntech/intervene We use this to produce VCF UpSet plots for benchmarking

intervene upset --figtype png --type genomic -i vcf1 vcf2 vcf3 --save-overlaps --filenames --bedtools-options header