modules/gatk4_applybqsr

Apply base quality score recalibration (BQSR) to a bam file

bambase quality score recalibrationbqsrcramgatk4

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

Description

Apply base quality score recalibration (BQSR) to a bam file

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file from alignment

*.{bam,cram}

`input_index`
`:file`

BAI/CRAI file from alignment

*.{bai,crai}

`bqsr_table`
`:file`

Recalibration table from gatk4_baserecalibrator

`intervals`
`:file`

Bed file with the genomic regions included in the library (optional)

`fasta`
`:file`

The reference fasta file

*.fasta

`fai`
`:file`

Index of reference fasta file

*.fasta.fai

`dict`
`:file`

GATK sequence dictionary

*.dict

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`${prefix}.bam`
`:file`

Recalibrated BAM file

${prefix}.bam

`bai`

`meta`
`:map`

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

`${prefix}*bai`
`:file`

Recalibrated BAM index file

${prefix}*bai

`cram`

`meta`
`:map`

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

`${prefix}.cram`
`:file`

Recalibrated CRAM file

${prefix}.cram

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

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_applybqsr

Description

Input

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`bqsr_table`
`:file`

`intervals`
`:file`

`fasta`
`:file`

`fai`
`:file`

`dict`
`:file`

Output

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`bai`

`meta`
`:map`

`${prefix}*bai`
`:file`

`cram`

`meta`
`:map`

`${prefix}.cram`
`:file`

`versions`

`versions.yml`
`:file`

Tools

gatk4
Apache-2.0

included in

maintainers

get in touch

modules/gatk4_applybqsr

Description

Input

meta:map

input:file

input_index:file

bqsr_table:file

intervals:file

fasta:file

fai:file

dict:file

Output

bam

meta:map

${prefix}.bam:file

bai

meta:map

${prefix}*bai:file

cram

meta:map

${prefix}.cram:file

versions

versions.yml:file

Tools

gatk4 Apache-2.0

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`bqsr_table`
`:file`

`intervals`
`:file`

`fasta`
`:file`

`fai`
`:file`

`dict`
`:file`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`bai`

`meta`
`:map`

`${prefix}*bai`
`:file`

`cram`

`meta`
`:map`

`${prefix}.cram`
`:file`

`versions`

`versions.yml`
`:file`

gatk4
Apache-2.0