conda install -c bioconda bedtools -y conda install -c bioconda snpeff -y conda install -c bioconda bcftools -y conda install -c bioconda freebayes -y conda install -c bioconda varscan -y conda install -c bioconda gatk -y conda install -c bioconda gatk4 -y # GenomeAnalysisTK -h 与ga...
>conda install -c bioconda package_name Packages can be updated with: >conda update package_name In general, because conda only performs the smallest set of updates in order to satisfy the dependency graph, it isstrongly advisedto always update the environment as a whole afterwards: ...
python RTDmaker.py ShortReads --assemblies </path/to/assembly-folder> --references </path/to/references-folder> --SJ-data </path/to/SJ-folder> --SJ-reads <2,1> --genome <genome.fasta> --fastq </path/to/fastq-folder> --tpm <1, 1> --fragment-len <0.7> --antisense-len <0.5>...
fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA -- Statistics bedcov read depth per BED region depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck) -- Viewing flags explain BAM flags tview ...