Description
merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.
Input
either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used.
*.vcf.gz
path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode.
/path/to/existing/gendb
file containing the intervals to be used when creating the genomicsdb
*.interval_list
if an intervals file has not been spcified, the value enetered here will be used as an interval via the “-L” argument
example: chr1:1000-10000
Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.
true/false
Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.
true/false
Output
Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db
*/$prefix
Directory containing the files that compose the updated genomicsdb workspace, this is only output for update mode, and should be the same path as the input wspace.
same/path/as/wspace
File containing the intervals used to generate the genomicsdb, only created by get intervals mode.
*.interval_list
