ApplyBQSR (doc)
apply base quality score recalibration.
- {sample}.bam, {reference}.fasta, recalibrated_data.table -> {sample}.recalibrated.bam
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'