1?????? 介紹
PennCNV是一個免費軟件工具，可從SNP基因分型陣列檢測拷貝數變異（CNV）。目前，它可以處理來自Illumina和Affymetrix陣列的信號強度數據。通過適當準備文件格式，它還可以處理其他類型的SNP陣列和寡核苷酸陣列。PennCNV實現了一個隱藏的馬爾可夫模型（HMM），該模型集成了多種信息源，以推斷單個基因型樣本的CNV調用。官網為：http://penncnv.openbioinformatics.org/en/latest/
2?????? 安裝準備
華為云購買一臺鯤鵬服務器
本文以云服務器KC1實例搭建，云服務器配置如表1-1所示。
表1-1?云服務器配置
項目
說明
規格
kc1.large.2 ? | 4vCPUs | 8GB
磁盤
系統盤：高IO（40GB）
操作系統要求如表1-2所示。
表1-2?操作系統要求
項目
說明
-
CentOS
7.6
在公共鏡像中已提供。
Kernel
4.14.0
在公共鏡像中已提供。
3?????? 配置編譯環境
安裝依賴包。
yum?install?perl-devel?perl-devel?-y
配置perl環境
在文件/etc/profile末尾添加如下內容。
export?C_INCLUDE_PATH=$C_INCLUDE_PATH:?/usr/lib64/perl5/CORE
2. 按Esc，并且輸入wq!保存退出。
3. 輸入如下命令，使環境變量生效。
source?/etc/profile
4?????? 安裝PennCNV
安裝
配置PennCNV環境
在文件/etc/profile末尾添加如下內容。
export PATH=$PATH:/usr/local/src/PennCNV-1.0.5
按Esc，并且輸入wq!保存退出。
輸入如下命令，使環境變量生效。
source /etc/profile
5?????? 運行和驗證
1）進入example目錄。
cd?/usr/local/src/PennCNV-1.0.5/example
2）執行程序runex.pl。
當系統回顯類似如下信息時，表示PennCNV安裝成功。
[root@ecs?example]#?perl?runex.pl?? ?Usage:? ??????runex.pl?<1|2|3|4|5|6|7|8|9|10|11|12|13|14|15|16>? ?? ??????Optional?arguments:? ?????????????-v,?--verbose???????????????????use?verbose?output? ?????????????-h,?--help??????????????????????print?help?message? ?????????????-m,?--man???????????????????????print?complete?documentation? ?????????????????--path_detect_cnv???????????path?to?detect_cnv.pl? ?????????????????--path_visualize_cnv????????path?to?visualize_cnv.pl? ?????????????????--path_convert_cnv??????????path?to?convert_cnv.pl? ?????????????????--path_filter_cnv???????????path?to?filter_cnv.pl? ?????????????????--path_compare_cnv??????????path?to?compare_cnv.pl? ?? ??????Function:?test-drive?PennCNV?and?related?scripts?in?your?system? ?? ??????Example:?runex.pl?1?(run?PennCNV?to?call?CNV?on?three?signal?files)? ???????????????runex.pl?2?(run?posterior?CNV?calling?algorithm?on?a?trio)? ???????????????runex.pl?3?(run?PennCNV?with?GCmodel?adjustment?of?signal?intensity)? ???????????????runex.pl?4?(validation-based?CNV?calling?on?a?candidate?region)? ???????????????runex.pl?5?(validation-based?CNV?calling?on?all?candidate?regions?in?a?file)? ???????????????runex.pl?6?(run?joint?CNV?calling?on?a?trio)? ???????????????runex.pl?7?(convert?CNV?call?to?BED?format)? ???????????????runex.pl?8?(convert?CNV?call?to?tab-delimited?format)? ???????????????runex.pl?9?(convert?tab-delimited?calls?to?PennCNV?format)? ???????????????runex.pl?10?(filter?CNV?and?print?out?a?subset?of?calls)? ???????????????runex.pl?11?(compare?CNV?calls?on?duplicated?samples)? ???????????????runex.pl?12?(compare?CNV?calls?on?same?sample?called?by?different?algorithms)? ???????????????runex.pl?13?(generate?CNV-based?genotype?calls)? ???????????????runex.pl?14?(validate?de?novo?CNV?calls?and?assign?a?P-value)? ???????????????runex.pl?15?(convert?Canary?CNV?calls?to?PennCNV?format)? ???????????????runex.pl?16?(plot?signal?intensity?for?CNV?calls?in?JPG?formats)
3、用戶可以嘗試一一運行這些示例，并對PennCNV可以做什么以及如何使用命令行選項有所了解。 例如，讓我們先嘗試第一個示例：
[root@ecs?example]#?perl?runex.pl?1? ?Exercise?1:?individual-based?calling?and?write?the?output?to?ex1.rawcnv? ?????????Running?command?? ?? ?******************************************************************************? ?NOTICE:?All?program?notification/warning?messages?that?appear?in?STDERR?will?be?also?written?to?log?file?ex1.log? ?NOTICE:?Reading?marker?coordinates?and?population?frequency?of?B?allele?(PFB)?from?../lib/hh550.hg18.pfb?...?Done?with?566108?records?(178?records?in?chr?M,XY?were?discarded)? ?NOTICE:?Reading?LRR?and?BAF?values?for?from?father.txt?...?Done?with?93129?records?in?4?chromosomes? ?NOTICE:?Data?from?chromosome?X?will?not?be?used?in?analysis? ?NOTICE:?Median-adjusting?LRR?values?for?all?autosome?markers?from?father.txt?by?0.0221? ?NOTICE:?Median-adjusting?BAF?values?for?all?autosome?markers?from?father.txt?by?0.0029? ?NOTICE:?quality?summary?for?father.txt:?LRR_mean=0.0027?LRR_median=0.0000?LRR_SD=0.1335?BAF_mean=0.5063?BAF_median=0.5000?BAF_SD=0.0390?BAF_DRIFT=0.000037?WF=0.0184?GCWF=0.0136? ?NOTICE:?Reading?LRR?and?BAF?values?for?from?mother.txt?...?Done?with?93129?records?in?4?chromosomes? ?NOTICE:?Data?from?chromosome?X?will?not?be?used?in?analysis? ?NOTICE:?Median-adjusting?LRR?values?for?all?autosome?markers?from?mother.txt?by?-0.0199? ?NOTICE:?Median-adjusting?BAF?values?for?all?autosome?markers?from?mother.txt?by?0.0324? ?NOTICE:?quality?summary?for?mother.txt:?LRR_mean=0.0039?LRR_median=0.0000?LRR_SD=0.1374?BAF_mean=0.5044?BAF_median=0.5000?BAF_SD=0.0418?BAF_DRIFT=0.000140?WF=0.0100?GCWF=0.0028? ?NOTICE:?Reading?LRR?and?BAF?values?for?from?offspring.txt?...?Done?with?93129?records?in?4?chromosomes? ?NOTICE:?Data?from?chromosome?X?will?not?be?used?in?analysis? ?NOTICE:?Median-adjusting?LRR?values?for?all?autosome?markers?from?offspring.txt?by?-0.0087? ?NOTICE:?Median-adjusting?BAF?values?for?all?autosome?markers?from?offspring.txt?by?0.0260? ?NOTICE:?quality?summary?for?offspring.txt:?LRR_mean=0.0028?LRR_median=0.0000?LRR_SD=0.1263?BAF_mean=0.5045?BAF_median=0.5000?BAF_SD=0.0429?BAF_DRIFT=0.000293?WF=-0.0171?GCWF=-0.0100? ?? ?******************************************************************************
6?????? 故障排除
問題：編譯報“error: 'off64_t' does not name a type”錯誤
問題描述：
進入“PennCNV-1.0.5/kext”目錄，執行make時，提示信息如圖所示。
問題原因：
off64_t屬于c++的類型，編譯時候需要用g++，而不是gcc。
解決方法：
修改Makefile，將編譯標志gcc改為g++，然后重新編譯。Makefile修改后如下：
CC = g++
LD = g++
基因測序 鯤鵬
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