BCFtools installation | Merge BAM files #bioinformatics #tutorial

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. 1️⃣ Search "bcftools download" 2️⃣ Go to 🔗https://www.htslib.org/download/ bcftools-1.22.tar.bz2 3️⃣ Installation cd bcftools-1.22 ./configure --prefix=/home/alex/Downloads/bcf_install make make install 4️⃣ Install throughout the system (optional) export PATH=/home/alex/Downloads/bcf_install/bin:$PATH 5️⃣ You may need this command to troubleshoot ./configure --prefix=/home/alex/Downloads/bcf_install --disable-bz2 --disable-lzma --disable-libcurl 6️⃣ Samtools Merge samtools merge --threads 3 -o AS_WO_ETOH.bam SRR30685383_MD.bam SRR30685384_MD.bam SRR30685385_MD.bam samtools merge --threads 3 -o AS_W_ETOH.bam SRR30685389_MD.bam SRR30685390_MD.bam SRR30685391_MD.bam ✉️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 in 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 how to install bcftool, how to merge bam files, bcftool tutorial, bam merge tutorial, system wide installation, variant analysis, variant calls, vcf, bcf, variant call format, snp analysis, snp call, deletion analysis, bcftools installation, bcftools tutorial, bcftools Linux, bcftools command line, install bcftools, bcftools conda, bcftools bioconda, merge bam files, bam file merging, merge bam bcftools, bam file processing, bam file tutorial, sam bam files, 🏷️ 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, #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