modules/gatk4_getpileupsummaries

Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.

gatk4germlinevariantsitesgetpileupsumariesreadcountssummary

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

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file to be summarised.

*.{bam,cram}

`index`
`:file`

Index file for the input BAM/CRAM file.

*.{bam.bai,cram.crai}

`intervals`
`:file`

File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.

*.interval_list

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fasta`
`:file`

The reference fasta file

*.fasta

`meta3`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fai`
`:file`

Index of reference fasta file

*.fasta.fai

`meta4`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`dict`
`:file`

GATK sequence dictionary

*.dict

`variants`
`:file`

Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.

*.vcf.gz

`variants_tbi`
`:file`

Index file for the germline resource.

*.vcf.gz.tbi

Output

name:type

description

pattern

`table`

`meta`
`:map`

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

`*.pileups.table`
`:file`

Table containing read counts for each site.

*.pileups.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_getpileupsummaries

Description

Input

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`variants`
`:file`

`variants_tbi`
`:file`

Output

`table`

`meta`
`:map`

`*.pileups.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

maintainer

get in touch

modules/gatk4_getpileupsummaries

Description

Input

meta:map

input:file

index:file

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

variants:file

variants_tbi:file

Output

table

meta:map

*.pileups.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

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`variants`
`:file`

`variants_tbi`
`:file`

`table`

`meta`
`:map`

`*.pileups.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