Strategy for samples run across different lane
i need to ask is this the right strategy for multilane samples. i saw in many papers
data run across different lanes aligned to the hg19, build 37) using bwa-0.7.10 (MEM algorithm)
merged using Picard version1.104.
PCR duplicates marked using Mark Duplicates. After all these pre-processing steps, GATK (Genome analysis tool kit-version 3.3) is used for local realignment, Base quality score recalibration and genetic variations extraction