Variant Annotation and effect prediction with snpeff

Variant effect prediction and annotation wth snpeff | Bacterial Genomes *Thank me with a Coffee* https://www.buymeacoffee.com/informatician https://www.paypal.com/paypalme/theinformatician *Teaching*(Video Conferencing): https://calendly.com/bioinformaticscoach *Consultation*(Video Conferencing): https://calendly.com/bioinformaticscoach *Consultation*(Audio Call): https://clarity.fm/vincentappiah *Reach out* [email protected] Subscribe to my channels Bioinformatics: https://www.youtube.com/channel/UCOJM9xzqDc6-43j2x_vXqCQ Data Science: https://www.youtube.com/channel/UC3bjbWYK7S_FLW0y0Ux4tyQ Short Clips: https://www.youtube.com/channel/UCrJE3zmKNdkmPsh_6TIPIIg datasets: https://github.com/vappiah/bioinformatics-tutorials/tree/main/variant-annotation/datasets/vcfs/bacteria/mycobacterium_ulcerans_isolate download snpeff: https://pcingola.github.io/SnpEff/download/ snpeff options: https://pcingola.github.io/SnpEff/se_commandline/ snpeff : https://pcingola.github.io/SnpEff/se_inputoutput/ snippy: https://github.com/tseemann/snippy/tree/master How to install bcfools conda: https://youtu.be/BLhVqBXL_v4 build from source: https://youtu.be/EJGz3yryrPo How to Install JAVA https://youtu.be/q9ZuBJVfAfU https://youtu.be/kISRCTzaaHc 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 Bacterial variant effect prediction wth snpeff Variant Effect Prediction with VCF Variant Effect Prediction with VCF in snpeff Variant Effect Prediction with VC snpeff and cfff bioinformatics for beginners bioinformatics tutorial bioinformatics course Bioinformatics Project #bioinformaticsforbeginners #bioinformatics #bioinformática #linuxforbeginners #linux