GATK Data Pre-processing

GATK is a Genome Analysis Toolkit. Here are some notes about GATK:

GATK data pre-processing

GATK data pre-processing

Here is a workflow from GATK:

1. Raw Mapped Reads (Bam) -> MarkDuplicates Check and compare results

samtools view BEFORE_MARKDUPLICATES.bam | wc -l
samtools view AFTER_MARKDUPLICATES.bam | wc -l

2. -> BaseRecalibrator + ApplyBQSR -> Analysis-Ready Rads (Bam)