gtc2vcf
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How to get Call_Freq, AAfreq, BBfreq, and AB Freq
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
- "Call Freq" < 0.97
- "AA Freq" = 1 AND "AA T Mean" > 0.3
- "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