Description

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

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’]

vcf (list)

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

tbi (list)

list of tbi files that match with the input vcf files

*.vcf.gz_tbi

wspace (file)

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

interval_file (file)

file containing the intervals to be used when creating the genomicsdb

*.interval_list

interval_value (string)

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

run_intlist (boolean)

Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.

true/false

run_updatewspace (boolean)

Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.

true/false

input_map (boolean)

Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb.

*.sample_map

Output

Name (Type)
Description
Pattern

genomicsdb (directory)

Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db

*/$prefix

updatedb (directory)

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

intervallist (file)

File containing the intervals used to generate the genomicsdb, only created by get intervals mode.

*.interval_list

versions (file)

File containing software versions

versions.yml
included in
createpanelrefs rnadnavar sarek
maintainer
Github user GCJMackenzie
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gatk4

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590