input文件是 exon_probe.hg38.gene.bed,见我前面的教程(数据处理过程中有的是意外),制作得到 targets.preprocessed.interval.list 这个文件后面需要用,如下: 代码语言:javascript 代码运行次数:0 运行 AI代码解释 tail /home/jianmingzeng/biosoft/GATK/resources/bundle/hg38/cnv/targets.preprocessed.interval.list ch...
input文件是exon_probe.hg38.gene.bed,见我前面的教程(数据处理过程中有的是意外),制作得到targets.preprocessed.interval.list这个文件后面需要用,如下: tail /home/jianmingzeng/biosoft/GATK/resources/bundle/hg38/cnv/targets.preprocessed.interval.list chrY2486896924869539+ . chrY2489543824896008+ . chrY2489625524...
本次更新支持基因组版本切换hg19/hg38,以及项目bed文件;方便各种项目切换和适配以及bug修复 最近准备为sliverworkspace 图形化生信平台开发报告设计器,需要一个较为复杂的pipeline作为测试数据,就想起来把之前的 [[满分室间质评之GATK Somatic SNV+Indel+CNV+SV(下)性能优化]]翻出来用一下。跑了一遍发现还是各种问题...
my_fusion_candidates <- c("../5.fusion_from_fq/SRR11178348/star-fusion.fusion_predictions.abridged.tsv") my_fusions <- import_starfusion(my_fusion_candidates, "hg38") 在示例代码中,使用了 get_fusion_by_id 通过id来获取单独的融合基因事件,我们这里就直接对列表操作[[1]]取第一个 edb 代码...
3下载后的hg38的bwa_index文件夹内有以下文件: 代码语言:javascript 代码运行次数:0 运行 AI代码解释 kelly@DESKTOP-MRA1M1F:/mnt/f/kelly/bioTree/server/wesproject/hg38$ tree-h.├──[1.8G]1000G_phase1.snps.high_confidence.hg38.vcf.gz ├──[2.0M]1000G_phase1.snps.high_confidence.hg38.vcf...
这个流程内置了一个hg38的参数模板,内容如下 AI检测代码解析 { "##_COMMENT1": "SAMPLE NAME AND UNMAPPED BAMS", "PreProcessingForVariantDiscovery_GATK4.sample_name": "NA12878", "PreProcessingForVariantDiscovery_GATK4.ref_name": "hg38",
Since many common references such as hg38 have N's at the very beginning of the autosomes and X/Y, many pipelines will not be affected by this bug. However, users of a telomere-to-telomere reference, users doing mitochondrial calling, and users with reads aligned to the alt sequences wil...
the primary assembly coordinates are identical for loci but patch updates differ. Also, the naming conventions of the references differ, e.g. the use of chr1 versus 1 to indicate chromosome 1, such that these also require lift-over to compare data. GRCh38/hg38 unifies the assemblies and ...
gatk4 --java-options"-Xmx10G -Djava.io.tmpdir=${tmpDir}"PrintReads \-R hg38.fa \#参考序列,若输入文件为bam文件,可省略此参数-L chrM \#指定线粒体染色体--read-filter MateOnSameContigOrNoMappedMateReadFilter \#Keep only reads whose mate...
本次更新支持基因组版本切换hg19/hg38,以及项目bed文件;方便各种项目切换和适配以及bug修复 最近准备为sliverworkspace 图形化生信平台开发报告设计器,需要一个较为复杂的pipeline作为测试数据,就想起来把之前的 [[满分室间质评之GATK Somatic SNV+Indel+CNV+SV(下)性能优化]]翻出来用一下。跑了一遍发现还是各种问题...