Chrom os

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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And 2), Inkling (Color Variants), Daisy, Ridley, Simon Belmont, Richter Belmont, Chrom, Dark Samus, King K. Rool, Isabelle, Ken Masters, Incineroar, Piranha Plant (Petey Piranha), Joker (Arsène) , Hero (III, IV, VIII and XI), Banjo & Kazooie, Terry Bogard, Byleth (Sothis), Min Min, Minecraftian (Steve, Alex, Zombie and Enderman) Sephiroth, Aegises (Pyra and Mythra) and Kazuya Mishima renders belong to Super Smash Bros. Ultimate www.smashbros.com/en_US/Cappy render belongs to toasted912 www.deviantart.com/toasted912/…Ultra Sword render belongs to water-kirby www.deviantart.com/water-kirby…Paula, Poo, Super Sonic and Chrom renders belongs to Nibroc-Rock www.deviantart.com/nibroc-rockToad render belongs to Nintega-Dario www.deviantart.com/nintega-dar…Bread logo belongs to YoshiMan1118 www.deviantart.com/yoshiman111…MegaMewtwo Y render belongs Arrancon www.deviantart.com/arrancon/ga…F.L.U.D.D., Triforce, Ancient Bow, Link’s Bows, Link’s Boomerangs, Yoshi Egg, Arwing, Polutergust 5000, Ghost Plunger, YoYo, Blue Falcon, Peaches and Flowers, Pterodactyl, Ice, Sheikah Symbol, Phantom, Pills, Pill Formation, Milk, Doriyah Sword, Critical Hit, Cape, Grand Chariot, Wario Bike, Garlic, Rocketbarrel Booster, Peanut Popgun, Gordo, Waddle Dee, Sonic’s Spring, Pikmin, Hocotate Ship, Gyro, Wolfen, Lloid Rocket, Tree, Villager’s Axe, Tom Nook, Timmy & Tommy, Wii Fit Poses, Balance Board, Wii Rings, Starbits, Ring, Grand Super Star, KO, Water Shuriken, Black Hole and Mega Laser, Riki, Dark Pit’s Staff, Wild Gunmen, Can, Hadoken, Limit Gauge, Corrin Dragon Form, Gomorrah, Ink Tank, Killer Wail, Daisies, Blue Toad, Daisy’s Umbrella, Vampire Killer, Cross, Holy Water, Axe, Dagger, Coffin, Blast-O-Matic, Balloon, Stop Sign, Belt, Ropes, Ptooie, Hero (DQ), Hero (DQ II), Hero (DQ V), Hero (DQ VI), Hero (DQ VII), Hero (DQ IX) and Hero (DQ X), Slime, Jinjos, Mighty Jinjonator, Jiggy, Egg, Banjo,

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