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+ | ====== Instructions ====== | ||
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+ | PSYC 7102 -- Statistical Genetics. Final Exam | ||
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+ | **Due:** December 17 2015 @ 5pm. | ||
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+ | There are 5 questions, each worth 8 points, for a total of 40 possible points. The exam is "open book". Use whatever online sources are helpful to you. All questions contain multiple parts -- please read the questions carefully and answer all components. | ||
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+ | Complete this exam on your own, without help from others. | ||
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+ | For this final exam I ask that you conduct all requested analyses on the following files, each of which contains a single person from 1000 Genomes. There' | ||
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+ | / | ||
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+ | ====== Question 1 ====== | ||
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+ | Interpret the phenotypic effects of variant rs16969968. | ||
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+ | - Tell me the location, alleles, genotype, dosage, and number of reads at this site for HG00096 (1 point) | ||
+ | - What is the functional effect of the alternate allele at this site? (1 point) | ||
+ | - How does this variant impact HG00096' | ||
+ | - Use samtools to interactively visualize the reads at this site for HG00096 and describe the output for rs16969968. Include a screenshot. You will have to do some googling to understand the output! (4 points) | ||
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+ | Here is an example samtools visualization command: | ||
+ | samtools tview -p chr:pos -d C in.bam / | ||
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+ | |||
+ | ====== Question 2 ====== | ||
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+ | This section will draw from the quality control plots of a bad Illumina run here: http:// | ||
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+ | - Look at the per tile sequence quality plot. Tell me what this type of plot represents, generally, and what this specific plot tells us about the sequencing run. (1 point) | ||
+ | - Do the same for the Kmer Content plot and table. (1 point) | ||
+ | - Looking at all the plots, what do you think caused the problems in this run? Why? (2 points) | ||
+ | - Give me the command to print out lines in a gzipped BAM file that correspond to reads where at least one base has the lowest possible alignment quality score. (Think regex) (4 points) | ||
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+ | ====== Question 3 ====== | ||
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+ | What do genetic ancestry PCA estimates, such as those you generated in this course, represent (3 points)? In your opinion how is genetic ancestry different from/ | ||
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+ | ====== Question 4 ====== | ||
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+ | Describe the difference between coding and regulatory variation and summarize their relative roles in complex traits and diseases. (8 points) | ||
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+ | ====== Question 5 ====== | ||
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+ | On a conceptual level, how does imputation work (2 points)? List and discuss three advantages of conducting imputation in genetic association studies (6 points). |