Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below.

Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index.

-O

-a, -c, -m

-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO.

-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]

-S. File of sample names to include. One sample per line.

-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)

-h. File containing lines to append to VCF header.

-i, -e. Include/ exclude sites for which expression is true. Must use valid expression.

--rename-chrs. File containing chromosome renaming map, with "old_name new_name\n" pairs separated by whitespaces, each on a separate line.

-x. Comma-separated list of annotations to remove.