def recalibrate_quality(sort_bam_file, fastq1, fastq2, sam_ref, config):
"""Recalibrate alignments with GATK and provide pdf summary.
"""
dbsnp_file = _get_dbsnp_file(config, sam_ref)
recal_file = gatk_recalibrate(sort_bam_file, sam_ref, config, dbsnp_file)
_analyze_recalibration(recal_file, fastq1, fastq2)
return recal_file
def recalibrate_quality(sort_bam_file, fastq1, fastq2, sam_ref, dirs, config):
"""Recalibrate alignments with GATK and provide pdf summary.
"""
dbsnp_file = configured_ref_file("dbsnp", config, sam_ref)
recal_file = gatk_recalibrate(sort_bam_file, sam_ref, config, dbsnp_file)
if config["algorithm"].get("recalibration_plots", False):
_analyze_recalibration(recal_file, fastq1, fastq2, dirs, config)
return recal_file
def recalibrate_quality(sort_bam_file, fastq1, fastq2, sam_ref,
dirs, config):
"""Recalibrate alignments with GATK and provide pdf summary.
"""
dbsnp_file = configured_ref_file("dbsnp", config, sam_ref)
recal_file = gatk_recalibrate(sort_bam_file, sam_ref, config, dbsnp_file)
if config["algorithm"].get("recalibration_plots", False):
_analyze_recalibration(recal_file, fastq1, fastq2, dirs, config)
return recal_file