Variant Annotation and effect prediction with snpeff

Variant effect prediction and annotation wth snpeff | Bacterial Genomes

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download snpeff: https://pcingola.github.io/SnpEff/dow...
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snpeff : https://pcingola.github.io/SnpEff/se_...
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00:00 Intro
00:41 Open the terminal
00:44 Create a working directory and cd into it
01:00 Download, Install and Set up snpEff
03:57 Download the example VCF data to be used for the variant effect prediction
08:14 Normalize the vcf file with bcftools
12:08 Check the available databases in snpeff for variant effect prediction
15:54 Download the snpeff database for our bacteria strain (Mycobacterium ulcerans)
18:56 Variant Effect Prediction with snpeff
22:50 Dealing with the issue "ERROR_CHROMOSOME_NOT_FOUND" in snpeff
39:54 Save the the snpeff result to an output file
40:50 Explore the Output
41:30 Generate Statistics Summary
42:30 Explore the Output




How to Predict variant effect prediction and annotation wth snpeff

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