GATK Installation | AddOrReplaceReadGroup | Variant analysis #bioinformatics #tutorial #genomics

The Genome Analysis Toolkit (GATK) is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data, and bundles the popular Picard toolkit. 1️⃣ Search GATK tool 2️⃣ Go to 🔗https://gatk.broadinstitute.org/hc/en-us 3️⃣ Download latest version of ###### Download the zip file 671 MB Download release: gatk-4.6.2.0.zip 4️⃣ Extract the package ⚠️⚠️⚠️ Make sure that your system has Java installed ⚠️⚠️⚠️ Java installation tutorial 🔗https://youtu.be/OgDRrEtQ4r8 5️⃣ In the GATK directory, open the terminal java -jar gatk-package-4.6.2.0-local.jar 6️⃣ Step 1 : Add or Replace Read Group java -jar gatk-package-4.6.2.0-local.jar AddOrReplaceReadGroups java -jar gatk-package-4.6.2.0-local.jar AddOrReplaceReadGroups -I SRR30685383.bam -O SRR30685383_ARRG.bam -PL ILLUMINA -PU unit1 -LB Alcohol_stress -SM WO_ETOH 📢📢📢📢📢 Download the total script from the github https://github.com/gravitiwork/StudyTech_scripts/tree/main/001_GATK_ARRG ✉️Email- [email protected] Email me for further contact 📢 Save my video URL on a notepad in your lab computer. So that you can get this video 📢 Subscribe to my Study tech YouTube channel. Because it is free for you but it will help me a lot. ====================== Follow genomic variants analysis pipeline ===================== ------ Tutorial made the year 2024-2025 🎯Step 1: Download fastq(raw file-SRA) file from NCBI https://youtu.be/LWYQZKRIQKk 🎯Step 2: Fastq file quality check [Fastqc tool] https://youtu.be/URyCysY15mI 🎯Step 3: Trim the adaptar and bad reads from the fastq file [Fastp tool] https://youtu.be/SAyerESRrDg 🎯Step 4: Mapping/Alignment of fastq to generate SAM file [STAR tool] https://youtu.be/OD4pBDFXGqY https://youtu.be/0KEaZwoGmg8 🎯Step 5: Sort the SAM file into BAM [ Samtools ] https://youtu.be/T2pE6T8VSBQ 🎯Step 6: AddOrReplaceReadGroup of BAM files [GATK tools] https://youtu.be/vR7nrKpV0f8 🎯Step 7: Mark Duplication of BAM files [GATK tools] https://youtu.be/IPGN4Iy6mw0 🎯Step 8: Merge BAM files [ Samtools ] https://youtu.be/XVmK0G8mQOI 🎯Step 9: mpileup for variant calling [ BCFtools ] https://youtu.be/4fIRQfkbBLo 🎯Step 10: snp analysis [snpEFF tools] https://youtu.be/XyCF2TH6N7M ====================== Subscribe to my channel, and learn complete genomics analysis 💻 System configuration Procession- Intel i5 4th gen, 1.7 GHz, 4 cpu(or thread) RAM-8GB Boot and working drive- 256GB SSD OS- Linux Mint 21.1 Cinnamon 📢 Guys, if you need any tutorial or help regarding Bioinformatics work, we will try to help you by Video or Chat. Fill free to ask in the comment section. If you are very new to Bioinformatics and have some very basic and silly questions. You are most welcome. Don't hesitate to ask us. You can write in the comment section. =========== Jump to 🏷️ Video specific tags how install gatk, gatk installation, install gatk, Genome Analysis Toolkit, gatk tutorial, gatk variant analysis, add or remove read group, Variant Calling pipeline, WGS Variant Calling, Variant Calling, gatk sofware install, gatk variant calling, gatk variant calling tutorial, gatk haplotype caller, gatk mutect2 tutorial, gatk installation tutorial, gatk install bam file, accession, bioproject, SRA, Fastq, sequence file, raw file, NCBI, biosample, GEO dataset, SNP, toolkit, NCBI toolkit, 🏷️ Channel tags transcriptomics, genomics, RNAseq, DNAseq,fasta, fastq, bam, sam, quality control and trimming, bioinformatic tutorial, tutorial,bioinfo, tool, software, package, linux, ubuntu synopsis, script, code, terminal,prompt, command, sequence alignment, sequence, bioinformatics training, file format, bioinformatics projects, Genomics, Molecular biology, Gene, DNA, RNA, Secondary analysis, Tertiary analysis, Gene regulations, Genetics, Human genome #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #ngs #python ♫♫♫♫♫♫ Music used in video ♫♫♫♫♫♫ mortals-feat-laura-brehm--future-trap--ncs---copyright-free-music Track: Warriyo - Mortals (feat. Laura Brehm) [NCS Release] Music provided by NoCopyrightSounds. Watch: http://NCS.lnk.to/MortalsAT/youtube Free Download / Stream: http://ncs.io/Mortals