vcf-merge - 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.