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Analyzing variants detected

VCF format has alternative Allele Frequency tags denoted by AF= Try the following command to see what frequency our variants exist at.

Code Block
grep AF1 SRR030257.vcf

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Expand
titleHow you would change this to variants that have a frequency of at least 90%?

Remember from our Raw Sequencing Data tutorial yesterday that we can group certain characters together by placing them between square brackets [].

Code Block
languagebash
title2 equivalent answers again
cat SRR030257.vcf | grep -v AF1=0.[0-8] > SRR030257.filtered.vcf

grep -v AF1=0.[0-8] SRR030257.vcf > SRR030257.filtered.vcf

Here we added a decimal point after the 0, and then allowed for a match to any digit between 0 and 8. Thus lines that have AF1=1 would not match, nor would a line with AF1=0.9 .


Return to GVA2020 course page.


Optional Exercises at the end of class or for Wednesday/Thursday choose your own tutorial time.

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