modules/gatk4_calculatecontamination

Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.

gatk4calculatecontaminationcross-samplecontaminationgetpileupsummariesfiltermutectcalls

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

Description

Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.

Input

name:type

description

pattern

`meta`
`:map`

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

`pileup`
`:file`

File containing the pileups summary table of a tumor sample to be used to calculate contamination.

*.pileups.table

`matched`
`:file`

File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input.

*.pileups.table

Output

name:type

description

pattern

`contamination`

`meta`
`:file`

File containing the contamination table.

*.contamination.table

`*.contamination.table`
`:file`

File containing the contamination table.

*.contamination.table

`segmentation`

`meta`
`:file`

File containing the contamination table.

*.contamination.table

`*.segmentation.table`
`:file`

output table containing segmentation of tumor minor allele fractions (optional)

*.segmentation.table

`versions_gatk4`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gatk4
Apache-2.0

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

modules/gatk4_calculatecontamination

Description

Input

`meta`
`:map`

`pileup`
`:file`

`matched`
`:file`

Output

`contamination`

`meta`
`:file`

`*.contamination.table`
`:file`

`segmentation`

`meta`
`:file`

`*.segmentation.table`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4
Apache-2.0

included in

maintainers

get in touch

modules/gatk4_calculatecontamination

Description

Input

meta:map

pileup:file

matched:file

Output

contamination

meta:file

*.contamination.table:file

segmentation

meta:file

*.segmentation.table:file

versions_gatk4

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Topics

versions

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Tools

gatk4 Apache-2.0

included in

maintainers

get in touch

`meta`
`:map`

`pileup`
`:file`

`matched`
`:file`

`contamination`

`meta`
`:file`

`*.contamination.table`
`:file`

`segmentation`

`meta`
`:file`

`*.segmentation.table`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

gatk4
Apache-2.0