BCFtools installation | Merge BAM files
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
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====================== Follow genomic variants analysis pipeline =====================
------ Tutorial made in the year 2024-2025
🎯Step 1: Download fastq(raw file-SRA) file from NCBI
• How to download fastq file | Full tutorial...
🎯Step 2: Fastq file quality check [Fastqc tool]
• How to install fastqc in windows | Beginne...
🎯Step 3: Trim the adapter and bad reads from the fastq file [Fastp tool]
• Fastp | Install | Run | Paired end #bioinf...
🎯Step 4: Mapping/Alignment of fastq to generate SAM file [STAR tool]
• STAR | Install | Build index | #bioinforma...
• STAR | sequence alignment | mapping #bioi...
🎯Step 5: Sort the SAM file into BAM [ Samtools ]
• Samtools | Install | SAM to BAM conversion...
🎯Step 6: AddOrReplaceReadGroup of BAM files [GATK tools]
• GATK Installation | AddOrReplaceReadGroup...
🎯Step 7: Mark Duplication of BAM files [GATK tools]
• GATK Tutorial | Mark Duplication | Varian...
🎯Step 8: Merge BAM files [ Samtools ]
• BCFtools installation | Merge BAM files #b...
🎯Step 9: mpileup for variant calling [ BCFtools ]
• BCFtools tutorial | mpileup | variant call...
🎯Step 10: snp analysis [snpEFF tools]
• snpEff tutorial | Installation | variant c...
====================== Subscribe to my channel, and learn complete genomics analysis
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