Helmholtz Zentrum München Institute of Human Genetics 10.07.2012

1. Institute of Human Genetics Variant Calling Helmholtz Zentrum München Institute of Human Genetics 10.07.2012

2. Methods HG00117 Lab7 BAM HG00355 Lab7 BAM NA06986 Lab7 BAM NA19095 Lab7 BAM NA20527 Lab7 BAM HG00117 Lab6 BAM HG00117 Lab6 BAM HG00117 Lab6 BAM HG00117 Lab6 BAM HG00117 Lab6 BAM HG00117 Lab5 BAM HG00117 Lab5 BAM HG00117 Lab5 BAM HG00117 Lab5 BAM HG00117 Lab5 BAM HG00117 Lab4 BAM HG00117 Lab4 BAM HG00117 Lab4 BAM HG00117 Lab4 BAM HG00117 Lab4 BAM HG00117 Lab3 BAM HG00117 Lab3 BAM HG00117 Lab3 BAM HG00117 Lab3 BAM HG00117 Lab3 BAM HG00117 Lab2 BAM HG00117 Lab2 BAM HG00117 Lab2 BAM HG00117 Lab2 BAM HG00117 Lab2 BAM HG00117 Lab1 BAM HG00117 Lab1 BAM HG00117 Lab1 BAM HG00117 Lab1 BAM HG00117 Lab1 BAM Samtools Multisample Variant Calling

3. Comparison with 1000G data • Filtering of 1000G Variants: • Gencode v12 Transcripts • Covered by at least one read in corresponding BAM files • Comparison of VCF files with custom Perl script • Output: • matching.vcf • not_matching.vcf • not_found.vcf

4. Comparison with 1000G data

5. Comparison with 1000G data CorrectGTs NotFoundGTs percent of variants percent of variants number of reads number of reads

6. Methods HG00117 Lab1 BAM HG00355 Lab1 BAM NA06986 Lab1 BAM NA19095 Lab1 BAM NA20527 Lab1 BAM Samtools Multisample VariantCalling HG00117 Lab2 BAM HG00355 Lab2 BAM NA06986 Lab2 BAM NA19095 Lab2 BAM NA20527 Lab2 BAM Samtools Multisample VariantCalling HG00117 Lab3 BAM HG00355 Lab3 BAM NA06986 Lab3 BAM NA19095 Lab3 BAM NA20527 Lab3 BAM Samtools Multisample VariantCalling …

7. Known RNA editing sites Li et al., Science, 2009

8. Future work • Multi Sample calling on all GEM BAM files • Systematic analysis of not_found/not_matching calls • Comparison with imputation data (and future phase 2 data) • Systematik calling of RNA editing sites (e.g. Ramaswami et al., Nature Methods, 2012)