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how to filter SNPs/Indels after VQSR

when I finished VQSR, I got a vcf file "recalibrated_variants.vcf",

[wubin]$ awk -F"\t" 'NR>161{print $7}' recalibrated_variants.vcf|sort|uniq -c
65902 LowQual
3163999 PASS
122377 VQSRTrancheINDEL90.00to99.00
53509 VQSRTrancheINDEL99.00to99.90
4589 VQSRTrancheINDEL99.90to100.00
742359 VQSRTrancheSNP90.00to99.00
368105 VQSRTrancheSNP99.00to99.90
184493 VQSRTrancheSNP99.90to100.00

If I want 99% truth sites sensitivity, I can discard sites of


and retain sites of


Am I right ?


Best Answer


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