modules/gatk4_genomicsdbimport

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

gatk4genomicsdbgenomicsdbimportjointgenotypingpanelofnormalscreation

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/genomicsdbimport

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

`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 specified, the value entered here will be used as an interval via the “-L” 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