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lab_1 [2017/04/13 10:32] scott |
lab_1 [2017/04/13 13:43] scott /* Example commands */ |
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### b) What is the allele frequency of this allele in individuals of African ancestry? | ### b) What is the allele frequency of this allele in individuals of African ancestry? | ||
### c) Is this SNP associated with any phenotypic effects? | ### c) Is this SNP associated with any phenotypic effects? | ||
+ | ### d) Describe the geographical distribution of allele frequency for this variant using | ||
+ | ### the website | ||
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### We can also grab both variants, if we wanted to | ### We can also grab both variants, if we wanted to | ||
grep -E ' | grep -E ' | ||
+ | |||
+ | ### What if we have a variant where we don't know the rsID, | ||
+ | ### but only the chromosome, position, genome build, and alleles? | ||
+ | ### Well, to get chromosome 1, position 11850759, we can do this: | ||
+ | grep -E ' | ||
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grep -E ' | grep -E ' | ||
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+ | ====== Useful databases ====== | ||
+ | |||
+ | |||
+ | **Geography of Genetic Variants Browser** Interactively browse geographic distribution of genetic variants. Can compare to 1000 Genomes, ExAC, and POPRES (Euro-centric). http:// | ||
+ | |||
+ | **dbSNP** A fairly exhaustive database of SNPs in humans. https:// | ||
+ | |||
+ | **ExAC** A good source for exonic variants. Very user friendly. http:// | ||