GATK Tutorial | Mark Duplication | 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. 📢📢📢📢📢 Check my previous video for Installation and Add or Replace Read Group 🔗https://youtu.be/vR7nrKpV0f8 📢 Script of this video 1️⃣ In the GATK directory, open the terminal java -jar gatk-package-4.6.2.0-local.jar MarkDuplicates 2️⃣ Step 1 : MarkDuplicates java -jar gatk-package-4.6.2.0-local.jar MarkDuplicates -I SRR30685383_ARRG.bam -O SRR30685383_MD.bam -M SRR30685383_Mtx.txt --REMOVE_DUPLICATES true --CREATE_INDEX true --VALIDATION_STRINGENCY SILENT 📢📢📢📢📢 Download the total script from the github https://github.com/gravitiwork/StudyTech_scripts/tree/main/001_GATK_ARRG https://github.com/gravitiwork/StudyTech_scripts/tree/main/002_GATK_MD ✉️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 adapter 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 mark duplication, 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