BioInformatics/Linux_Tools8 Bam Format Viewer - IGV (conda) ◆ Install >>> conda install bioconda::igv ◆ Usage >>> igv 1) Load file(bam) 2) Find gene or alignmend sequence 3) Zoom in 2024. 4. 3. VCF Annotation & Filtering - SnpEff & SnpSift(Bcftools) ▶ SnpEff & SnpSift ◆ Install # Download latest version >>> wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip # Unzip file >>> unzip snpEff_latest_core.zip ◆ Usage ※ Reference SNP.vcf가 .gz(압축파일)일때 >>> tabix -p vcf reference_snp.vcf.gz ● dbSNP 정보 추가(ID, INFO) >>> java -Xmx16g -jar snpEff/SnpSift.jar annotate reference_snp.vcf(.gz) input.vcf > output.vcf ※ Reference Database.. 2024. 4. 3. Variant Calling - Clair3 (conda) ◆ Install(python3.9환경) # make sure channels are added in conda >>> conda config --add channels defaults >>> conda config --add channels bioconda >>> conda config --add channels conda-forge # create conda environment named "clair3" # replace clair3 by clair3-illumina for using illumina data >>> conda create -n clair3 -c bioconda clair3 python=3.9.0 -y >>> conda activate clair3 # Install b.. 2024. 4. 3. Mapping - Bowtie2 & Samtools (conda) ◆ Install(python3.8환경) 1) 가상환경 설정 >>> conda create -n [환경명] python=3.8 >>> conda env list # 가상환경 리스트 출력 >>> conda activate [환경명] 2) 설치 >>> conda install bioconda::bowtie2 >>> conda install bioconda::samtools ◆ Usage 1. 가상환경 설정 >>> conda activate [환경명] 2. Reference Index >>> bowtie2-build reference.fasta 3. Mapping >>> bowtie2 -x reference.fasta -1 input_fwd.fastq -2 input_rev.fastq -S ou.. 2024. 4. 3. 이전 1 2 다음
