PLINKSEQ教程1

xiaoxiao2021-03-01  6

PLINK/SEQ教程1

学习PLINK/SEQ,基于一个toy VCF dataset。

使用帮助:

pseq help pseq help stats #pseq help {command}

PSEQ 使用:

pseq input-source command {--argument} #input-source指定VCF文件或者一个PLINK/Seq project [jiahuan@ln tutorials]$ pseq ex1.vcf v-view chr1:1001 rs1001 T/C . 1 PASS chr1:1002 rs1002 G/A . 1 PASS chr1:1003 rs1003 G/A . 1 PASS

col4=表示和T一样(教程里说的是consensus variant),col5=这个突变在几个样本里被观察到,col6=代表VCF里的Filter列

[jiahuan@ln tutorials]$ pseq help v-view v-view : view variant data --------------------------------------------------------- --geno { flag } show genotypes --gmeta { flag } show genotype meta-information --hide-null { flag } . --only-alt { flag } . --only-minor { flag } . --pheno . --samples { flag } show each specific sample variant --simple { flag } simple variant format, POS RET ALT --verbose { flag } verbose output --vmeta { flag } show variant meta-information [jiahuan@ln tutorials]$ pseq ex1.vcf v-view --vmeta --gmeta chr1:1001 rs1001 T/C . 1 PASS . VM=1;SM=100 P001 1 C/C [GM=1] P002 1 T/T [GM=2] P003 1 T/C [GM=3] P004 1 C/C [GM=4] P005 1 C/C [GM=5] chr1:1002 rs1002 G/A . 1 PASS . VM=2;SM=101 P001 1 A/A [GM=6] P002 1 G/A [GM=7] P003 1 G/A [GM=8] P004 1 A/A [GM=9] P005 1 A/A [GM=10] chr1:1003 rs1003 G/A . 1 PASS . VM=3;SM=102 P001 1 G/G [GM=11] P002 1 G/G [GM=12] P003 1 G/A [GM=13] P004 1 A/G [GM=14] P005 1 G/G [GM=15]

提取特定的突变,样本等,使用mask做筛选用:

[jiahuan@ln tutorials]$ pseq ex1.vcf v-view --gmeta --mask reg=chr1:1002 include="gf(GM>8)" indiv=P001,P003,P005 chr1:1002 rs1002 G/A . 1 PASS P001 1 ./. [GM=6] P003 1 ./. [GM=8] P005 1 A/A [GM=10]

counts可以统计minor allele出现次数:

[jiahuan@ln tutorials]$ pseq ex1.vcf counts VAR REF/ALT MINOR CNT TOT chr1:1001 T/C T 3 10 chr1:1002 G/A G 2 10 chr1:1003 G/A A 2 10

创建一个项目,导入,项目内统计:

[jiahuan@ln tutorials]$ pseq proj1 new-project #创建一个新的project Creating new project specification file [ proj1.pseq ] [jiahuan@ln tutorials]$ pseq proj1 load-vcf --vcf ex1.vcf #导入VCF loading : /work/home/jiahuan/tools/plinkseq-0.10/tutorials/ex1.vcf ( 5 individuals ) /work/home/jiahuan/tools/plinkseq-0.10/tutorials/ex1.vcf : inserted 3 variants [jiahuan@ln tutorials]$ pseq proj1 var-summary #统计project内突变和样本情况 ---Variant DB summary--- 3 unique variants File tag : 1 (3 variants, 5 individuals) [jiahuan@ln tutorials]$ pseq proj1 counts #基于project统计minor allele的情况 VAR REF/ALT MINOR CNT TOT chr1:1001 T/C T 3 10 chr1:1002 G/A G 2 10 chr1:1003 G/A A 2 10

参考

转载请注明原文地址: https://www.6miu.com/read-3650349.html

最新回复(0)