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lab_2

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lab_2 [2017/04/19 14:12]
scott 		lab_2 [2017/04/30 22:20]
scott /* Lab assignment 2 */
Line 73: Line 73:
 ### variant's allele frequency? ### variant's allele frequency?
  
 +
 +Example full credit answers
 +
 +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).
 +
 +zgrep -w 'rs671' hu916767_20170324191934.1kgALTallele.withHeader.snpEff.vcf.gz
 +
 + 12 112241766 rs671 G A . . ANN=A|missense_variant|MODERATE|ALDH2|ENSG00000111275|transcript|ENST00000261733|protein_coding|12/13|c.1510G>A|p.Glu504Lys|1571/2018|1510/1554|504/517||,A|missense_variant|MODERATE|ALDH2|ENSG00000111275|transcript|ENST00000416293|protein_coding|11/12|c.1369G>A|p.Glu457Lys|1465/1572|1369/1413|457/470||,A|3_prime_UTR_variant|MODIFIER|ALDH2|ENSG00000111275|transcript|ENST00000548536|nonsense_mediated_decay|13/14|c.*1386G>A|||||22035|,A|3_prime_UTR_variant|MODIFIER|ALDH2|ENSG00000111275|transcript|ENST00000549106|nonsense_mediated_decay|3/4|c.*89G>A|||||89|WARNING_TRANSCRIPT_NO_START_CODON GT 0/0
 +
 +This individuals has 0 alternate alleles, so their genotype is G/G. Two reference alleles.
 +
 +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.
 +
 +zgrep 'synonymous\|missense\|start_gain\|start_lost\|stop_gain\|stop_lost\|3_prime_UTR_variant\|5_prime_UTR_variant' hu916767_20170324191934.1kgALTallele.withHeader.snpEff.vcf.gz | wc -l
 +   52772
 +
 +
 +3. Coming soon
  
  
lab_2.txt · Last modified: 2017/05/02 09:09 by scott

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