Format converter

Rastair includes a convert subcommand that allows converting between many of the supported file formats.

Streaming

Rastair's convert command supports streaming input and output, so that it can be used in a pipeline with other commands. Since it only guesses the formats based on file names, they need to be specified explicitly when streaming.

For example, to convert the first entries from a VCF file to BED format you can use the following command:

head -n1000 test.vcf | rastair convert -f vcf -F bed | less

Possible conversions

Note that not all formats contain the same information. Rastair can only convert to formats that contain the same or less information than the source.

That means, for a given input, it can convert to a format in the same group or a lower group in this list:

1. Internal format (.mpk.lz4)

   Rastair's internal data structures, serialized. Contains all metrics in their original structure. Not guaranteed to be stable across versions.

2. VCF/BCF (.vcf/.vcf.gz, .bcf)

   Contains basically all information, serialized in a standard way. Can be processed using BCFtools.

3. BED (.bed) and per-read BED (.reads.bed)

   Contains the most important calling information. Can be processed using BEDtools (or anything else that can read tab-separated-values files).