Page Comparison

...

Expand

title	Test "genetic drift" vs. "functional selection" - e.g. is the distribution of variants different among non-coding regions, synonymous changes in coding regions, and non-synonymous changes in coding regions?

Compare the output of these three commands:

Code Block

grep intergenic NA12878.chrom20.samtools.vcf.genome_summary.csv | awk 'BEGIN {FS=","} {print $26"\t"$27}' | sort | uniq -c | sort -n -r | head -20
grep exonic NA12878.chrom20.samtools.vcf.genome_summary.csv | grep -w synonymous | awk 'BEGIN {FS=","} {print $25"\t"$26}' | sort | uniq -c | sort -n -r | head -20
grep exonic NA12878.chrom20.samtools.vcf.genome_summary.csv | grep -w nonsynonymous | awk 'BEGIN {FS=","} {print $25"\t"$26}' | sort | uniq -c | sort -n -r | head -20

Do you notice a pattern?

What's the right statistical test to determine whether non-synonymous mutations might be under different selective pressure than intergenic or synonymous mutations from this data?

Expand

title	Thinking back to our first example where we looked for a gene with 2 frameshift deletions, can you think of a way to look at all 3 patients' GATK analysis results at once, and look for the total number of mutations detected (sorted by gene) displayed in descending order?

The final form of the command that you had was:

grep "frameshift" NA12878.chrom20.GATK.vcf.exome_summary.csv | awk -F"," '{print $2"\t"$3}' | uniq -c | sort -r

Code Block

language	bash
title	Try to come up with a solution on your own before checking your answer here
collapse	true

cat *GATK.vcf.exome_summary.csv | grep "exonic" | awk -F"," '{print $2,"\t"$3}' | sort | uniq -c | sort -nr

Some questions for thought:

Why might this type of analysis be useful?
What other greps would make this more useful?

Other variant annotators:

...

Versions Compared

Old Version 5

New Version Current

Key

Other variant annotators: