本文介绍利用CrossMap对参考hg19基因组的VCF文件进行hg38转换。 conda create -n py3 python=3.6 conda activate py3 conda install -c bioconda pyBigWig conda install CrossMap mkdir data #在home/ding下面创建data文件夹 cd data #进入该文件夹,转换路径 下载hg19ToHg38.over.chain.gz 文件和参考基因组 Homo...
${chrom}.vcf.bgz fi done # 下载全部染色体的vcf文件 hg19, 59G wget -c https://gnomad-public-us-east-1.s3.amazonaws.com/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz else ### 下载hg38版本 exomes vcf ### for chrom in {1..22} X Y; do echo $chrom if [ ! -f...
在基因组数据分析中,变异类型的精准分类是理解疾病机制、筛选致病位点的关键步骤。今天我们要介绍的SnpSift Variant Type,就像是一个“快速标签机”,它能快速为VCF文件中的每个变异贴上"身份标签",让数据分析变得更加顺畅。 SnpSift Variant Type依赖三大工具协同工作: 1.SnpSift:作为核心工具,其对基因组变异进行各种分...
The default version of our dbSNP annotation is currently referring to dbSNP138 (using hg19 coordinates) as shown below. However, users can also retrieve older versions of dbSNP: db135, dbSNP129, dbSNP130, dbSNP131 and dbSNP132. The 129 and 130 versions use hg18 as a reference genome and 1...
By default, peddy uses hg19/GRCh37. It can be forced to use sites for hg38 by passing--sites hg38. To create custom sites, have a look atthe sites files included with peddyalong with the corresponding .bin.gz which is just the raw binary alternate counts (gt_types) from thousand-geno...
VCF file path, if NULL output to console #' @param refversion reference version, currently only support #' @param annoS SNP variant annotation, download if not given #' @param annoI Infinium-I variant annotation, download if not given #' hg19 and hg38 in human #' #' @return VCF file...
GRCh37.75 Homo_sapiens GRCh38.86 Homo_sapiens hg19 Homo_sapiens (USCS) hg19kg Homo_sapiens (UCSC KnownGenes) hg38 Homo_sapiens (USCS) hg38kg Homo_sapiens (UCSC KnownGenes) testHg19ChrM Homo_sapiens (UCSC) 然后当然是下载对应数据库,我选择的是GRCh37.75 java -jar snpEff.jar download GRCh37.75...
GRCh37.75 Homo_sapiens GRCh38.86 Homo_sapiens hg19 Homo_sapiens (USCS) hg19kg Homo_sapiens (UCSC KnownGenes) hg38 Homo_sapiens (USCS) hg38kg Homo_sapiens (UCSC KnownGenes) testHg19ChrM Homo_sapiens (UCSC) 然后当然是下载对应数据库,我选择的是GRCh37.75 java -jar snpEff.jar download GRCh37.75...
ucsc.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_...
hg38kg Homo_sapiens (UCSC KnownGenes) testHg19ChrM Homo_sapiens (UCSC) 然后当然是下载对应数据库,我选择的是GRCh37.75 java -jar snpEff.jar download GRCh37.75 注释 以GATK获得的snp的vcf文件为例,对其进行注释 java -Xmx4g -jar ~/biosoft/SnpEff/snpEff/snpEff.jar GRCh37.75 KPGP-00001_filtered_pa...