apply-bqsr

ApplyBQSR (doc)

apply base quality score recalibration.

IO

• {sample}.bam, {reference}.fasta, recalibrated_data.table -> {sample}.recalibrated.bam

Exmaple snakemake rules

rule apply_bqsr:
    input:
        bam = '{sample}.bam',
        reference = '{reference}.fasta',
        recalibration_table = '{sample}_recalibration.table',
    output:
        '{sample}.recalibrated.bam'
    params:
        # Optional parameters. Omit if unused.
        java_options = '-Xmx32g'
    threads: 1
    log: 'logs/gatk/apply-bqsr/{sample}.log'
    wrapper:
        'http://dohlee-bio.info:9193/gatk/preprocessing/apply-bqsr'