lab_2
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lab_2 [2017/04/19 08:38] scott /* What I've done to prepare the vcf file */ |
lab_2 [2017/04/30 22:20] scott /* Lab assignment 2 */ |
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| For another example, take rs6681049. The REF allele is T and the ALT is C. The genotype is 1/1. That means that one chromosome of this individual carries 1 ALT allele (i.e., a C) and the other chromosome also carries 1 ALT allele (i.e., a C). So the genotype for this individual at that site is C/C. | For another example, take rs6681049. The REF allele is T and the ALT is C. The genotype is 1/1. That means that one chromosome of this individual carries 1 ALT allele (i.e., a C) and the other chromosome also carries 1 ALT allele (i.e., a C). So the genotype for this individual at that site is C/C. | ||
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| + | ====== Lab assignment 2 ====== | ||
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| + | ### Lab 2 assignment | ||
| + | ### Assigned: 4/20/2017 | ||
| + | ### Due: 4/27/2017 at the beginning of class. Late assignments (even by 5 minutes) | ||
| + | ### will not be accepted! | ||
| + | ### | ||
| + | ### Note: all questions should be answered with respect to the | ||
| + | ### | ||
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| + | ### Question 1 (4 points) | ||
| + | ### a) Extract a variant from the vcf and show me the command you used | ||
| + | ### and the output of the command. Tell me what the individual' | ||
| + | ### genotype is at this site. | ||
| + | |||
| + | ### Question 2 (4 points) | ||
| + | ### How many variants did 23andMe genotype in exons; that is, in protein coding sequences. | ||
| + | ### Show me the commands you used to figure this out. | ||
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| + | ### Question 3 (8 points) | ||
| + | ### a) Is this individual likely to be lactose intolerant? Show me the | ||
| + | ### steps you used to figure this out. | ||
| + | ### b) Pick one of the variants you used to determine lactose | ||
| + | ### intolerance. What is the geographical distribution of this | ||
| + | ### variant' | ||
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| + | Example full credit answers | ||
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| + | 1. Most of you got this one right. The most common mistake was to include too much information and too many steps (although that generally did not cost you any points). | ||
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| + | zgrep -w ' | ||
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| + | | ||
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| + | This individuals has 0 alternate alleles, so their genotype is G/G. Two reference alleles. | ||
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| + | 2. There are multiple ways to answer this. One of the most straightforward is as follows, although we could quibble over whether I should have included any splicing variants. | ||
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| + | zgrep ' | ||
| + | 52772 | ||
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| + | 3. Coming soon | ||
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| 1. 23andMe format was converted to vcf format. | 1. 23andMe format was converted to vcf format. | ||
| - | bcftools convert --tsv2vcf hu916767_20170324191934.txt -f ~/Desktop/human_g1k_v37.fasta.gz -s hu916767_20170324191934 -Ob -o hu916767_20170324191934.bcf | + | bcftools convert --tsv2vcf hu916767_20170324191934.txt -f human_g1k_v37.fasta.gz -s hu916767_20170324191934 -Ob -o hu916767_20170324191934.bcf |
| bcftools view hu916767_20170324191934.bcf -O vcf | bgzip -c > hu916767_20170324191934.vcf.gz | bcftools view hu916767_20170324191934.bcf -O vcf | bgzip -c > hu916767_20170324191934.vcf.gz | ||
lab_2.txt · Last modified: 2017/05/02 09:09 by scott
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