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Exome site list comparison 822 Illumina samples

Exome site list comparison 822 Illumina samples. JL Rodriguez-Flores 2011-08-02. Exome call sets compared. Call sets based on BC Illumina/Mosaik BAMs BC ALL.wgs.bc_illumina_822.20110521.snps.exome.sites.vcf BCM ALL.BCM_Illumina_Mosaik_ontarget_plus50bp_822.20110521.snp.exome.sites.vcf

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Exome site list comparison 822 Illumina samples

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  1. Exome site list comparison822 Illumina samples JL Rodriguez-Flores 2011-08-02

  2. Exome call sets compared • Call sets based on BC Illumina/Mosaik BAMs • BC • ALL.wgs.bc_illumina_822.20110521.snps.exome.sites.vcf • BCM • ALL.BCM_Illumina_Mosaik_ontarget_plus50bp_822.20110521.snp.exome.sites.vcf • UMICH • ALL.wgs.umich_illumina_softfiltered.20110521.snps.exome.genotypes.vcf • WCMC • All.autosomal.wcmc_illumina_mosaik.20110521.snps.exome.sites.vcf • Call sets based on Broad Illumina/BWA BAMs • Broad • ALL.wgs.broad_illumina.20110521.snps_indels.exome.genotypes.vcf.gz

  3. WCMC call set • 482,280SNPs • Consensus target exons + 50bp • Autosomes (chr 1-22) • Overlap with databases • dbSNP 132 38.6% • HapMap 3 6.3% • Phase 1 consensus 67.2%

  4. Call set site list pairwise union * Totals for each call set along the diagonal

  5. Site list overlapBCM, BC, Broad, UMICH, WCMC

  6. Ts:Tv at SNPs with 1 alternate allele

  7. Population count INFO Tag • For each site in WCMC call set • List of populations where at least one alternate allele was observed • Relevant for filtering?

  8. Number of populations with SNP WCMC Call set SNP sites Number of populations with >=1 ALT allele ASW, YRI, GBR, TSI, CHB, CLM, LWK, MXL, CHS, PUR, JPT, FIN, CEU

  9. Progress on WCMC exome call set • Site list uploaded • Genotypes available mid-week

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