Bioinf-practice-BI

Snakefile for HW2 "Why Did I Get the Flu?"

Authors:

• Software: Karitskaya Polina, Kozlova Polina,
  Institute of Bioinformatics, Saint Petersburg, Russia.

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Table of Contents

• How to Install
• How to Run
• Features
• Requirements

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How to Install

• Clone the repository to your local machine using Git or download the Snakefile from the GitHub repository.

git clone git@github.com:Cinnamonness/Bioinf-practice-BI.git
cd Bioinf-practice-BI

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How to run

• Create working directory For example:

mkdir practice2
cd practice2

• Make sure the Snakefile is in your working directory. In this example, the Snakefile should be in the practice2 directory.

• Ensure that you have downloaded the reference sequence.fasta. It should be in your working directory.

• Ensure you have installed VarScan.v2.3.9.jar. It should be in your working directory.

• Change the absolute path in Snakefile (it is the first string). To know your absolute path you can use command:

pwd

• install snakemake:

pip install snakemake 

• Run the Snakefile using this command from your working directory:

snakemake -p --cores all  

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Features

This project includes the following features:

1. Data Download:

   • Downloads FastQ files from the SRA FTP server for different samples (SRR1705851, SRR1705858, SRR1705859, and SRR1705860).

2. Reference Indexing:

   • The reference genome (sequence.fasta) is indexed using BWA to generate required index files for alignment.

3. Alignment and Sorting:

   • Aligns FastQ files to the reference genome using BWA.
   • Sorts the resulting BAM files using Samtools for downstream processing.

4. MPileup Generation:

   • Generates MPileup files from the aligned BAM files using Samtools, which are used for variant calling.

5. Variant Calling:

   • Two levels of variant calling are supported:
     • Common Variants: Calls variants with a minimum frequency of 95% using VarScan.
     • Rare Variants: Calls variants with a minimum frequency of 0.1% using VarScan.

6. Parallel Processing:

   • Processes multiple samples in parallel using Snakemake's expand functionality, ensuring that the workflow runs efficiently for multiple samples (SRR1705858, SRR1705859, SRR1705860).

7. VCF Output:

   • Generates VCF files containing the variant calls for each sample, separated into two files: one for common variants and another for rare variants.

8. Sample-Specific Results:

   • Each sample's analysis (alignment, variant calling, etc.) is handled separately, allowing for easy scalability to more samples by adding them to the Snakefile.

9. Compatibility with VarScan:

   • Integration with VarScan for variant calling ensures high-quality SNP calling and variant analysis from high-depth sequencing data.

10. Efficient Data Management:

• All output files are neatly organized in the working directory, ensuring proper file management and easy retrieval of results.

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Requirements

1. snakemake 8.25.3

2. bwa 0.7.17-r1188

3. samtools 1.13

4. VarScan.v2.3.9