gnomAD v2.1.1数据集包含来自125,748个外显子组和15,708个全基因组的数据,所有这些数据都映射到GRCh 37/hg 19和GRCh 38/hg 38 两个版本的参考序列。 gnomAD hg19 gnomAD数据库hg19与hg39 VCF文件批量下载脚本 download.sh # 获取当前目录路径,下载文件至当前目录 current_dir=`pwd` # 下载参考基因组对应的...
WBBC,施一公当校长的西湖大学,共纳入~15000个样本,目前提供了hg19和hg38两个版本的数据下载。 WBBC网址:wbbc.westlake.edu.cn/do 1. 可用数据(汉人) 可用数据 WBBC网站 2. 批量下载数据(hg38/hg19) 后台下载 nohup sh download_WBBC.sh > download.log 2&>1 & # download_WBBC.sh for i in {1....
You will need the intervals file generated byvcf-liftover, herehg38ToHg19.over.chain.offset. chr=chr1 pos=1234567 file=hg38ToHg19.over.chain.offset offset=$(awk -v c=$chr -v p=$pos '$1==c && p>=$2 && p<=$3{print $4}' $file) echo $(( $pos + $offset )) ...
in which case the change in EHH is integrated over a constant. Human genetic maps for GRCh36 and GRCh37 (hg18 & hg19) can be found at:http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/. iHS by default interpolates SNV positions to genetic position (you don't need a genetic...
HG002_SNP.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=...
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 ...
import snakemake.io import os REF="/data/data/reference/refs/ucsc.hg19.fasta" HM="/data/data/variant_call/hapmap_3.3.hg19.sites.vcf" OMNI="/data/data/variant_call/1000G_omni2.5.hg19.sites.v 浏览62提问于2019-05-30得票数 0 回答已采纳...
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...
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 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=...