modules/gatk4_applybqsrspark

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

bambase quality score recalibrationbqsrcramgatk4spark

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

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

]

`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

`meta:map`

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

]

`versions:file`

File containing software versions

versions.yml

`bam:file`

Recalibrated BAM file

*.{bam}

`cram:file`

Recalibrated CRAM file

*.{cram}

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_applybqsrspark

Description

Input

`meta:map`

`input:file`

`input_index:file`

`bqsr_table:file`

`intervals:file`

`fasta:file`

`fai:file`

`dict:file`

Output

`meta:map`

`versions:file`

`bam:file`

`cram:file`

Tools

gatk4
Apache-2.0

included in

maintainers

get in touch

modules/gatk4_applybqsrspark

Description

Input

meta:map

input:file

input_index:file

bqsr_table:file

intervals:file

fasta:file

fai:file

dict:file

Output

meta:map

versions:file

bam:file

cram: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`

`meta:map`

`versions:file`

`bam:file`

`cram:file`

gatk4
Apache-2.0