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freeseek / gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
MIT License
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How to get Call_Freq, AAfreq, BBfreq, and AB Freq #42

Closed mansi800 closed 1 year ago

mansi800 commented 2 years ago

Hi thanks for the great tool. I have some query, I want to remove some poor quality snps from the vcf file. The filteration I want should be based the following threshold

  1. "Call Freq" < 0.97
  2. "AA Freq" = 1 AND "AA T Mean" > 0.3
  3. "BB Freq" = 1 AND BB T Dev" > 0.06

I can see that AA T Mean and BB T Dev are there in the VCF file but I am unable to find Call Freq, AA Freq, BB Freq and AB freq. Please let me know how can I get these values. Awaiting for your reply Thanks