This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Rerunning indel realignment and BQ score recalibration on already preprocessed files
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