bam_applybqsr

Apply Base Quality Score Recalibration (BQSR) to a BAM or CRAM file using GATK4 ApplyBQSR. Supports scatter-gather across genomic intervals: when more than one interval file is supplied per sample, the interval-level outputs are merged back together with samtools merge. When no intervals are supplied (num_intervals: 0), ApplyBQSR is run once on the whole input and no merge step is performed.

bamcrambqsrrecalibrationgatk4

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_applybqsr

Description

Input

name

description

pattern

`meta`

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

`meta2`

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

`intervals`

Bed file (or interval_list) with the genomic regions to restrict
recalibration to. Optional; pass [] if not used.

*.{bed,interval_list}

Output

name

description

pattern

`meta`

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

`versions`

File containing software versions

versions.yml

bam_applybqsr

Description

Input

`meta`

`meta2`

`intervals`

Output

`meta`

`versions`

included modules and subworkflows

maintainers

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