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:ā€˜testā€™]

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

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 ā€œ-Lā€ argument

example: chr1:1000-10000

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

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

meta:directory

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

*/$prefix

$prefix: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

meta: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

$updated_db: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

meta:file

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

*.interval_list

*.interval_list:file

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

*.interval_list

list:file

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

*.interval_list

versions

versions.yml:file

File containing software versions

versions.yml

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
included in
createpanelrefs sarek
maintainer
Github user GCJMackenzie
get in touch
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