Variant Calling for one gene - Stage of filtering
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14 days ago

Hi everyone,

I am interested in looking at variants of just one gene from RNASeq samples. For that, I am going to use the best practices from GATK for cases like this.

However, I was wondering: should I filter the bam files right after the alignment step and proceed with the pipeline with only the sequences for that gene or should I only filter in the VCF? Or at a different stage?

Thanks in advance!

André

gatk picard variant-calling • 102 views
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