Hi All,
I have cases and controls the were exomed sequenced and used GATK to call the variants in all the cases and controls combined. This generated a single vcf file with all the variants. I would like then to keep the variants that are in cases and not in my controls after removing the low quality variants (with scores < 30). I would like to get some ideas on the best way to handle this? The goal is to remove the variant s in the controls and see what is left.
thanks
I have cases and controls the were exomed sequenced and used GATK to call the variants in all the cases and controls combined. This generated a single vcf file with all the variants. I would like then to keep the variants that are in cases and not in my controls after removing the low quality variants (with scores < 30). I would like to get some ideas on the best way to handle this? The goal is to remove the variant s in the controls and see what is left.
thanks
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