4.1 NJ法构建进化树 # 生成dnadist需要的配置文件 echo -e "sequences.phy\nY" > dnadist.cfg #...
data(CEUData) #Creates a data frame 'CEUSNP' of genotype data and a vector 'CEUDist' #of physical locations of the SNPs # Produce a heat map in a grey color scheme MyHeatmap <- LDheatmap(CEUSNP, genetic.distances = CEUDist, color = grey.colors(20)) # Same heatmap, flipped below...
4.1 NJ法构建进化树 # 生成dnadist需要的配置文件 echo -e "sequences.phy\nY" > dnadist.cfg # 运行dnadist生成距离矩阵文件 dnadist < dnadist.cfg >dnadist.log # 生成neighbor程序需要的配置文件 mv outfile infile.dist echo -e "infile.dist\nY" > neighbor.cfg # 生成neighbor程序需要的配置文件 m...
6.绘制进化树 使用VCF2Dis 软件快速计算样品距离矩阵,直接到FastME网页基于距离矩阵,直接输入sample.vcf.dist文件绘制进化树 wget https://github.com/BGI-shenzhen/VCF2Dis/archive/refs/tags/1.44.zip unzip1.44.zip chmod-R a+xVCF2Dis-1.44/./VCF2Dis-1.44/bin/VCF2Dis-InPutdirect.vcf-OutPutsample.vcf....
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01. read alignment, sort, and remove PCR duplication 这一步也就是我们常用的数据处理了,包括比对、排序、标记PCR重复 bwa mem -t 4 -M -R '@RG\tID:$sample\tLB:$group\tPL:ILLUMINA\tSM:$sample' $reference.fa $fastq1 $fastq2 | samtools view -b -S -o $sample.bam ...
snp-dists833.10.332.833.133.7 psdm1617.60.217.417.518.0 snp-dists1620.70.220.420.721.1 Contributing Contributions are always welcome. For changes to be accepted, they must pass the CI and coverage checks. These include: Code is formatted (cargo fmt). ...
\n";my%hashRef;my%hashAlt;while(<RS>) {$_=~ s/[\r\n]//g;nextifnot /^rs/;my@array=split/\t/;$hashRef{$array[0]} =$array[1];#$hash{"rs"} = "ref";$hashAlt{$array[0]}{$array[1]} =$array[2];#$hashAlt{"rs"}{"ref"} = "alt";}openGENOTYPE,$snp_genotypeordie"...
library("LDheatmap")#读入数据SNP<-read.csv("CEUSNP.csv",header=TRUE)pos<-read.csv("CEUDist.csv",header=TRUE)#查看数据head(pos)SNP[1:4,1:4 二 绘制连锁不平衡图 2.1 直接绘制 代码语言:javascript 代码运行次数:0 复制 Cloud Studio代码运行 ...
链接:https://pan.baidu.com/s/1VxgJK5asCEjukOeA1V5rlg提取码:e69n head -n 5 test.ped | cat - <(tail -n 5 test.ped) > a && mv a test.ped 3、参考 下面文章进行 构建进化树https://zhuanlan.zhihu.com/p/85978856 样本ID必须是10个字符,这点很重要!!!使用如下命令修改: ...