Currently, the 'variant convert' command line contains '--to-avro', '--to-parquet', '--to-json',... parameters, they can be grouped in one parameter --to {avro | parquet | json}. In addition, the command line should offer some basic filters (e.g., region filter, quality filter,...) and it lacks of some important Parquet parameters (e.g. page size, row group size) to take into account:
Currently, the 'variant convert' command line contains '--to-avro', '--to-parquet', '--to-json',... parameters, they can be grouped in one parameter --to {avro | parquet | json}. In addition, the command line should offer some basic filters (e.g., region filter, quality filter,...) and it lacks of some important Parquet parameters (e.g. page size, row group size) to take into account:
./hpg-bigdata.sh variant convert -i .... -o .... --to {avro | parquet | json} [--from {vcf|avro}] --compression {deflate | snappy | ...} --data-model {opencb|ga4gh} [--page-size ...] [--row-group-size ...] [--include-formats ....] [--region ....] [--region-file ....] [--qual ....] [--filter ....] [--only-with-id]