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3.12. Base quality recalibration
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Several post-alignment processing steps are recommended to improve alignment accuracy around indels and reduce quality score bias. These will be performed with the Genome Analysis Toolkit (GATK), using the dbSNP VCF listed in section 2.4:
Important: Repeat steps 3.9 to 3.12 for the matched normal sample, beginning with 123456_N_R1.fastq.gz and 123456_N_R2.fastq.gz and ending with 123456_N_recal.bam.
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