Question: repeat BQSR and Indel realign
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zhou • 0 wrote:
Dear all, I copied bam files of tumor-normal pairs from others and conducted base quality recalibration and indel realign according to GATK best practice. Then I called variants by UnifiedGenotyper,followed by some filters.However,I found the bams had been handled with BQSR and Indelrealign by my colleagues. So many faults for the first analysis! I would like to know the effect of repeated BQSR and realign on variant calling and false positive rate?
Many thanks!