GWAS 质量控制（QC）分析流程

Use preset environment

目录

1、Install a Linux virtual machine or a Windows subsystem, open a terminal.

2、Download the key and connect to the server in the terminal.

3、Go to target dir and make your own data folder (minxian as an example)

4、Decompress the data and start the analysis

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1、Install a Linux virtual machine or a Windows subsystem, open a terminal.

You can find the tutorial somewhere else in this section.

2、Download the key and connect to the server in the terminal.

chmod 700 xh1eshell.hpccube.com_1107221622_rsa.txt
ssh -i xh1eshell.hpccube.com_1107221622_rsa.txt -p 65073 [email protected]
# Type yes when ask
#The authenticity of host '[xh1eshell.hpccube.com]:65073 ([218.26.37.181]:65073)' can't be established.
#ED25519 key fingerprint is SHA256:SRE9uDeyQyPSLAtITTfW7F1qwySmxXbGFAKCWJJDkP4.
#This key is not known by any other names
#Are you sure you want to continue connecting (yes/no/[fingerprint])? yes
#Warning: Permanently added '[xh1eshell.hpccube.com]:65073' (ED25519) to the list of known hosts.

链接: https://pan.baidu.com/s/1i0lxU-wXZ08sSRT71kh-1Q?pwd=14fr 提取码: 14fr 
--来自百度网盘超级会员v2的分享

3、Go to target dir and make your own data folder (minxian as an example)

# Use minxian as an example
cd /public1/share/ac7m4df1o5/chenxy/data
mkdir minxian
cd minxian
# load the cond preset env
conda activate qc

4、Decompress the data and start the analysis

cat ../raw-GWA-data.tgz | perl -pe 's/\r\n\z/\n/' | tar xfvz -
plink --ped raw-GWA-data.ped --map raw-GWA-data.map --make-bed --out raw-GWA-data

# check sex mis-match
plink --bfile raw-GWA-data --check-sex --out raw-GWA-data
cat raw-GWA-data.sexcheck | grep -i problem
# 772  772            2            0      PROBLEM       0.3084
# 853  853            2            0      PROBLEM       0.3666
#1920 1920            2            0      PROBLEM       0.4066