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mhmtgenc started a topic No mutations in BAM (IGV) but a mutation in final VCF?

in Bioinformatics

04-11-2018, 02:37 AM
No mutations in BAM (IGV) but a mutation in final VCF?

I use GATK 4.0 for the variant calling pipeline. my steps involve MarkDuplicates, BaseRecalibration, ApplyBaseRecalibration and HaplotypeCaller. When...

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