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

`input`

BAM or CRAM file to recalibrate, its index, and the recalibration
table produced by GATK4 BaseRecalibrator.

Structure: [ val(meta), path(reads), path(index), path(recal) ]

*.{bam,cram}

`references`

Reference genome fasta file, its index, and the GATK sequence dictionary.

Structure: [ val(meta2), path(fasta), path(fai), path(dict) ]

`intervals`

Bed file (or interval_list) with the genomic regions to restrict
recalibration to, together with the number of interval files being
processed for this sample. Pass [ [], 0 ] to run without intervals.

Structure: [ path(intervals), val(num_intervals) ]

*.{bed,interval_list}

`output_suffix`

Output file type, either ‘bam’ or ‘cram’.

Output

name

description

pattern

`recal_out`

Recalibrated BAM or CRAM file and its index. If more than one interval
was used, this is the merged output; otherwise it is the direct
ApplyBQSR output.

Structure: [ val(meta), path(reads), path(index) ]