snpEff tutorial | Installation | variant calling

SnpEff

Genetic variant annotation, and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).

1️⃣ Search "snpEff"

https://pcingola.github.io/SnpEff/

2️⃣ Download the file

snpEff_latest_core.zip

3️⃣ Unzip and Check

java -jar snpEff.jar


4️⃣ Database information

java -jar snpEff.jar databases database.txt


5️⃣ Now search for "Saccharomyces cerevisiae"


Saccharomyces_cerevisiae


6️⃣ Download the data


java -jar snpEff.jar download Saccharomyces_cerevisiae

6️⃣ Run


java -Xmx8g -jar snpEff.jar -v -canon Saccharomyces_cerevisiae -csvStats result AS_W_ETOH_calls.vcf AS_W_ETOH_calls_annotate.vcf


#### An additional parameter to add to our command is Xmx8G, a Java parameter to define available memory.


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====================== Follow genomic variants analysis pipeline =====================
------ Tutorial made in the year 2024-2025

🎯Step 1: Download fastq(raw file-SRA) file from NCBI
   • How to download fastq file | Full tutorial...  

🎯Step 2: Fastq file quality check [Fastqc tool]
   • How to install fastqc in windows | Beginne...  

🎯Step 3: Trim the adapter and bad reads from the fastq file [Fastp tool]
   • Fastp | Install | Run | Paired end #bioinf...  

🎯Step 4: Mapping/Alignment of fastq to generate SAM file [STAR tool]
   • STAR | Install | Build index | #bioinforma...  
   • STAR | sequence alignment | mapping  #bioi...  

🎯Step 5: Sort the SAM file into BAM [ Samtools ]
   • Samtools | Install | SAM to BAM conversion...  

🎯Step 6: AddOrReplaceReadGroup of BAM files [GATK tools]
   • GATK Installation  | AddOrReplaceReadGroup...  

🎯Step 7: Mark Duplication of BAM files [GATK tools]
   • GATK Tutorial  | Mark Duplication | Varian...  

🎯Step 8: Merge BAM files [ Samtools ]
   • BCFtools installation | Merge BAM files #b...  

🎯Step 9: mpileup for variant calling [ BCFtools ]
   • BCFtools tutorial | mpileup | variant call...  

🎯Step 10: snp analysis [snpEFF tools]
   • snpEff tutorial | Installation | variant c...  

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=========== Jump to

00:05 Introduction
00:54 Installation of snpEff
03:20 View snpEff database
05:37 Download snpEff database
07:18 Annotation vcf in to result
10:16 Description of snpEff result


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🏷️ Channel tags

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#ncbi #genomics #beginners #tutorial #howto #omics #research #biology #ngs #python