Zaki

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Zaki
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  • @Geraldine_VdAuwera Dear Geraldine, Could I ask.. Once a .bam has been realigned and recalibrated with GATK tool (Base Recalibration), is it safe to re-apply SortSam & ReorderSam on the .bam file? Would the re-application of SortSam & Reord…
  • @Geraldine_VdAuwera Thank you very much for your kind clarification. Could I extend my question to get an important concept corrected... I am slightly confused how would one decide what samples to combine in order to run Haplotype Caller, Is there…
  • @Geraldine_VdAuwera Could I ask, is VQSR meant to be run on a pooled vcf? Ie - for example if i have 20 vcf (since Haplotype was run individually on each sample [20 cancer cell line] ), should I ; 1) Combine the 20 vcf into one and run VQSR OR 2) …