Yuze · ✭
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- Yutze Li
@shlee Thanks! I will start new question thread the next time. Will it be fine if I run a leading HaplotypeCaller call first and use the output VCF to do BQSR to generate recalibrated BAM, and then use this BAM to do a final HaplotypeCaller call?
Hello, I am dealing with WGS data of fission yeast Sz. pombe. Is that fine to pass the VCF downloaded from Ensembl-fungi to BQSR as known variants? The VCF format is a little bit different from gatk output, for example the insertions are denoted as:…