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best practices and filter on small exome experiment

dcittarodcittaro Member Posts: 31
edited January 2013 in Ask the GATK team

Hi all, I have a 4 exome experiment (high coverage). According to best practices I can't apply VQSR, so I must filter on SNP properties. One thing is not clear: should all the option apply? In other words should I select using boolean "and" (i.e. QD  < 2.0 & MQ < 40.0 & FS > 60.0 & HaplotypeScore > 13.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0 for SNP) or "or" (i.e. QD  < 2.0 | MQ < 40.0 | FS > 60.0 | HaplotypeScore > 13.0 | MQRankSum < -12.5 | ReadPosRankSum < -8.0 for SNP)?

Post edited by Geraldine_VdAuwera on
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