CLI Reference

vcfpartition

Output bcftools region strings that partition the indexed VCF/BCF files into either an approximate number of parts (-n), or parts of approximately a given size (-s). One of -n or -s must be supplied.

If multiple VCF/BCF files are provided, the number of parts (-n) is interpreted as the total number of partitions across all the files, and the partitions are distributed evenly among the files.

Note that both the number of partitions and sizes are a target, and the returned number of partitions may not exactly correspond. In particular, there is a maximum level of granularity determined by the associated index which cannot be exceeded.

Note also that the partitions returned may vary considerably in the number of records that they contain.

vcfpartition [OPTIONS] VCFS...

Options

--version

Show the version and exit.

-v, --verbose

Increase verbosity

-n, --num-partitions <num_partitions>

Target number of partitions to split into

-s, --partition-size <partition_size>

Target (compressed) size of VCF partitions, e.g. 100KB, 10MiB, 1G.

Arguments

VCFS

Required argument(s)