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1000G Phase 1 Release chr20 call sets Ryan Poplin Genome Sequencing and Analysis Medical and Population Genetics January 25, 2011.

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Presentation on theme: "1000G Phase 1 Release chr20 call sets Ryan Poplin Genome Sequencing and Analysis Medical and Population Genetics January 25, 2011."— Presentation transcript:

1 1000G Phase 1 Release chr20 call sets Ryan Poplin Genome Sequencing and Analysis Medical and Population Genetics January 25, 2011

2 Data and Definitions -- Pipeline 2 Full indel cleaning process including known indels BAQ calculation using GATK implementation of H. Li Called by main continental AP and by admixed+ AP Variant quality score recalibration Quality cut chosen using HapMap3.3 + Omni 2.5M chip sensitivity Cut at 99.2% of accessible sites Not yet done genotype refinement

3 Data and Definitions – 1004 Samples 3 ASN=CHB + CHS + JPT ASN+= CHB + CHS + JPT + MXL + CLM + PUR EUR=CEU + FIN + GBR + TSI + IBS EUR+=CEU + FIN + GBR + TSI + IBS + MXL + CLM + PUR + ASW AFR=LWK + YRI + ASW AFR+= LWK + YRI + ASW + CLM + PUR AMR=MXL + CLM + PUR AMR+=MXL + CLM + PUR + ASW Note these definitions differ from the other groups

4 # samples Analysis Panel Total # variants dbSNP % (129) # knowns Known ti/tv # novels Novel ti/tv Novel non-CpG ti/tv 266ASN264,79350.02132,4482.32132,3452.241.72 427ASN+446,07938.61172,2482.35273,8312.301.79 351EUR300,11150.08150,3002.33149,8112.361.83 563EUR+516,41335.47183,1712.34333,2422.311.82 226AFR475,64137.50178,3912.35297,2502.361.85 331AFR+529,72634.82184,4282.35345,2982.381.86 161AMR350,46748.04168,3602.35182,1072.321.84 212AMR+452,25539.72179,6302.35272,6252.361.84 Final chr20 callsets including fragment-based calling and contrastive VQSR clustering

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