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Working with VCF Files using BCFToolsThis documentation outlines steps to manage VCF files, including compressing, indexing, querying chromosomes, counting variants, and comparing multiple VCF files using BCFTools. The provided instructions are formatted for use on an HPC (High-Performance Computing) environment.1. Creating and Activating a Conda EnvironmentFirst, create and activate a Conda environment for installing and running BCFTools.# Create a Conda environmentconda create --name myenv# Activate the Conda environmentconda activate myenv# Install BCFToolsconda install -c bioconda bcftools2. Compressing and Indexing VCF FilesTo efficiently manage large VCF files, compress and index them using bgzip and tabix.# Compress the .vcf file using bgzipbgzip filename.vcf# Create a tabix index file for the bgzip-compressed VCFtabix -p vcf filename.vcf.gz# Create an index for the VCF filebcftools index filename.vcf.gz3. Querying Chromosomes from VCF FilesRetrieve and save the list of unique chromosomes present in the VCF file. chromosomes.txt# Display the contents of the text filecat chromosomes.txt"># Query all chromosomes listbcftools query -f '%CHROM\n' filename.vcf.gz# Count the total number of unique chromosomesbcftools query -f '%CHROM\n' filename.vcf.gz | uniq | wc -l# Save the list of unique chromosomes in a text filebcftools query -f '%CHROM\n' filename.vcf.gz | uniq > chromosomes.txt# Display the contents of the text filecat chromosomes.txt4. Counting Variants per ChromosomeCreate a shell script to count all variants/mutations per chromosome and save it as chromosome_count.sh.# Create a .sh filetouch chromosome_count.sh# Edit the .sh file using nanonano chromosome_count.sh# Add the following content to the file#!/bin/bashchromlist=($(cat chromosomes.txt))for chrom in ${chromlist[@]}; do count=$(bcftools view -r $chrom filename.vcf.gz | grep -v -c '^#') echo "$chrom:$count"done5. Finding Common Variants Among Multiple VCF FilesUse BCFTools to find common variants among multiple VCF files.# Find common variants among three VCF filesbcftools isec -n=3 filename1.snps.vcf.gz filename2.snps.vcf.gz filename3.snps.vcf.gz | wc -l6. Filtering Variants with a "PASS" StatusRetain only the variants that have a filter status of "PASS". output.vcf">#

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