[code] diff 程式碼 === ###### tags: `Parabricks-v3.5` ###### tags: `基因體`, `NVIDIA`, `Clara`, `Parabricks`, `二級分析`, `Azure` <br> [TOC] <br> ## pbrun/pbargs.py - [v3.1.1](http://10.78.26.44:30000/Tj_Tsai/parabricks/-/blob/master/v3.1.1/pbrun/pbargs.py) - [v3.5.0](http://10.78.26.44:30000/Tj_Tsai/parabricks/-/blob/master/v3.5.0/pbrun/pbargs.py) ### 移除工具 ```= creategenomicsdb - Start a genomic database for multiple samples importgvcftodb - Add samples to a genomic database selectvariants - Select variants from database and create a gvcf ``` ### 新增工具 ```= samtoolsmpileup - Generate text pileup for one or multiple bam files bcftoolsmpileup - Generate bcf/vcf pileup for one or multiple bam files bcftoolscall - Call variants from mpileup output somaticsniper - Identify single nucleotide positions that are different between tumor and normal bam files somaticsniper_workflow - Run the somaticsniper variant caller workflow manta - Analyze germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs strelka - Analyze germline variation in small cohorts and somatic variation in tumor/normal sample pairs strelka_workflow - Run the strelka variant caller workflow glnexus - Merge and joint-call input gVCF files, emitting multi-sample BCF vcfqc - Run QC on the generated VCF ```