modules/gatk4_genomicsdbimport
merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.
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