VCFtools是一个用于处理和分析VCF格式文件的软件包。平均杂合度是指一个个体在某个位点上具有两种不同等位基因的数量的平均值。 在VCFtools中,可以通过以下命令来计算平均杂合度: ``` vcftools --vcf input.vcf --het ``` 这将计算出每个个体的平均杂合度,并将结果输出到一个文件中。你也可以通过添加`--out...
其它计算 –het Calculates a measure of heterozygosity on a per-individual basis. –hardy 每个位点的哈温平衡计算的Pvalue。 –TajimaD INT Tajima’s D 计算 –indv-freq-burden:calculates the number of variants within each individual of a specific frequency. –LROH Long Runs of Homozygosity –relat...
root@DESKTOP-1N42TVH:/home/test3#lsplink.hwe plink.log plink.nosex result.map result.ped root@DESKTOP-1N42TVH:/home/test3# head plink.hwe## 期待杂合度CHR SNP TEST A1 A2 GENO O(HET)E(HET)P1oar3_OAR1_17218 ALL(NP) G A9/105/2930.2580.256511oar3_OAR1_20658 ALL(NP) C A25/12...
vcftools--gzvcf output.vcf.gz--hardy--out output.hardy.txt output.hardy.txt文件的第三列为(HOM1/HET/HOM2),即等位1纯合基因型的个数/杂合基因型的个数/等位2纯合基因型的个数。运用perl脚本计算每个位点的缺失率、杂合率及MAF,stat_mr_het_maf.pl: <>;my$total=200;#群体个数print"Chr\tPos\tMR...
–het Calculates a measure of heterozygosity on a per-individual basis. Specfically, the inbreeding coefficient, F, is estimated for each individual using a method of moments. The resulting file has the suffix “.het”. –hardy Reports a p-value for each site from a Hardy-Weinberg Equilibriu...
Calculates a measure of heterozygosity on a per-individual basis. Specfically, the inbreeding coefficient, F, is estimated for each individual using a method of moments. The resulting file has the suffix ".het". --hardy Reports a p-value for each site from a Hardy-Weinberg Equilibrium test...
–het –hardy –site-quality 主要用于提取VCF文件中每个位点的QUAL信``` --missing-indv --missing-site 计算每个位点的缺失率 vcftools--vcftest.recode.vcf--missing-site--outms AI代码助手复制代码 –SNPdensity <integer>计算SNP在设定bin内的密度</integer> ...
--het Calculates a measure of heterozygosity on a per-individual basis. Specfically, the inbreeding coefficient, F, is estimated for each individual using a method of moments. The resulting file has the suffix '.het'. --hardy Reports a p-value for each site from a Hardy-Weinberg ...
$ lsx each_site_hardy.hwe|head-n2CHRPOSOBS(HOM1/HET/HOM2)E(HOM1/HET/HOM2)ChiSq_HWEP_HWEP_HET_DEFICITP_HET_EXCESSchr11146710239/8/0239.06/7.87/0.066.692747e-021.000000e+001.000000e+009.440689e-01 3.其它参数说明 3.1 基本选项 --vcf | --gzvcf | --bcf 输入格式,三选一即可 ...
.TA101.53PASSAC=2;AF=0.125;AN=16;BaseQRankSum=-2.261;ClippingRankSum=0;DP=239;ExcessHet=3.3099;FS=4.905;MLEAC=2;MLEAF=0.125;MQ=80.42;MQRankSum=0;QD=2.21;ReadPosRankSum=-0.033;SOR=1.609chrA01chrA01C2635.31PASSAC=6;AF=0.375_T_C:,_T_CchrA01931.AGAC=8;AF:,:35:921_T_C:267,0...