vcf-merge(1) merge the bgzipped and tabix indexed VCF files


merge-vcf [OPTIONS] file1.vcf file2.vcf.gz ... > out.vcf


About: Merge the bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)


-c, --chromosomes <list|file>
Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future.
-d, --remove-duplicates
If there should be two consecutive rows with the same chr:pos, print only the first one.
-H, --vcf-header <file>
Use the VCF header
-h, -?, --help
This help message.
-r, --regions <list|file>
Do only the given regions (comma-separated list or one region per line in a file).
-s, --silent
Try to be a bit more silent, no warnings about duplicate lines.