示例1 deftest_next_with_GT(self):"""Parse a file which already in Genotype format"""vcf_filename=os.path.join(test_data(),'file_with_SNPs_in_GT_format.aln.vcf')vcf_file=open(vcf_filename,'r')reader=SNPSitesReader(vcf_file)record=reader.next()samples=record.samples samples_with_alte...
SNP-dCAPS-Fnu4HI,330-gcngc-298-0163LEFT2792980YES2060.17955.00.00.04.70.0cttcacggcaatcacttcGc gCgaagtgattgccgtgaag0.2916276.814.00L8 SNP-dCAPS-Fnu4HI,330-gcngc-298-0163RIGHT4414220YES2059.88855.00.00.03.360.0ggaaaggttgctgggaggaa ttcctcccagcaacctttcc0.2916276.814.00R2 Sites that can differallfor...
示例\实例: #Create founder haplotypesfounderPop = quickHaplo(nInd=10, nChr=1, segSites=15)#Set simulation parametersSP = SimParam$new(founderPop)SP$addTraitA(10)SP$addSnpChip(5)#Create populationpop = newPop(founderPop, simParam=SP)pullSnpHaplo(pop, simParam=SP)...
转录因子结合位点 Transcription factor binding sites identified by ChIP-seq in ENCODE project SNP 位点上下 10bp 区域的保守性得分 PhyP scores of 46 vertebrates and 33 mammals across the +/-10bp region surrounding the SNP 总而言之,对于例子中的 rs12740374,我们可以看到关于这个突变的总分主要在于 TFBS...
SNP-dCAPS-Fnu4HI,330-gcngc-298-0 163 RIGHT 441 422 0 YES 20 59.888 55.0 0.0 0.0 3.36 0.0 ggaaaggttgctgggaggaa ttcctcccagcaacctttcc 0.291627 6.81 4.00 R2 Sites that can differ all for SNP CAPS cut information for snp SNP Enzyme Enzyme_seq Change_pos Other_cut_pos ...
*pFst <<"var_num"<<"\t"<<"scaffold"<<"\t"<<"Start"<<"\t"<<"End"<<"\t"<<"Fst"<<"\t"<<"Dxy_onlyVaiants"<<"\t"<<"Dxy_AllSites"<<"\t"<<"windowSize"<<std::endl;if(opt::regAbove >0) *regionsAboveFstFile <<"scaffold"<<"\t"<<"Start"<<"\t"<<"End"<<std:...
输出文件chr5D:9950377.txt示例:#Marker Enzyme Total size Restriction Sites Expected Fragments MembersPredicted CAPS candidates ---chr5D:9950377 AbaCIII 301 153 153,148 Altchr5D:9950377 AbaCIII 301 301 Refchr5D:9950377 AciI 301 148 153,148 Altchr5D:9950377 AciI 301 301 Refchr5D:9950377 BscGI ...
链接:https://pan.baidu.com/s/1eJGIOs2O8cULYbAbc83JCA 密码:ru01 输出文件chr5D:9950377.txt示例:#Marker Enzyme Total size Restriction Sites Expected Fragments Members Predicted CAPS candidates --- chr5D:9950377 AbaCIII 301 153 153,148 Alt chr5D:9950377 AbaCIII 301 301 Ref...
因为最近有一项工作是比较填充准确性的,中间有用到vcftools比较两个vcf文件. 使用命令也很简单: 1 vcftools --vcf file1.snp.vcf --diff file2.snp.vcf --diff-site --out Diff.site 运行结束会生成一个名为Diff.site.diff.sites_in_files的文件: pso1,ref1和alt1代表file1.snp.vcf文件中位点信息,IN_...