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Filteration creteria

i want to filter a vcf file resulted GATK. my criterias are QUAL < 30, FS > 60, MQ < 30, DP < 10 and GQ < 30.
filterExpression in my command line in GATK must be as following? GQ is in right place in command? another question is QD < 2 is good criteria for quality filteration?

--filterExpression "QUAL < 30 || FS > 60.0 || MQ < 30.0 || DP < 10 || GQ < 30"

thanks in advance

Best Answer


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