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problems with how to set stand_call_conf

Hi

I have several samples, some with a coverage of around 14, some with a coverage around 6. I want to use UnifiedGenotyper for SNP calling but I have no clue how to set stand_call_conf (and stand_emit_conf) as it is suggested to set stand_call_conf for samples with coverage >10 to 30 and for samples with coverage <10 to Q4. So how should I procede?

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Answers

  • i geraldine, thaks for the fast reply! sadly there is no set of known SNPs.... so i cant realy use VQSR....

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