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Rerunning indel realignment and BQ score recalibration on already preprocessed files

apolyakapolyak State College, PA, USAMember

Hi everyone!

I have these bam files, and I forgot to use the known feild (-known gold_indels.vcf) in the RealignerTargetCreater and BaseQualityScoreRecalibration walkers. I have fastq files, and I have the final bam file created after the complete preprocessing pipeline. I was hoping to just run my final bam file back through these walkers. Is this possible, or should I start over from fastqs? (I deleted the bam files from previous steps to save space)

Thanks for your help

Best Answer


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