CNV
使用软件 CNVnator_v0.3.2
过滤脚本 cnvnator_filter.pl
CNV输出结果
CNV_type coordinates CNV_size normalized_RD p-val1 p-val2 p-val3 p-val4 q0 duplication chr10:1-9590600 9.5906e+06 3.73714e+07 0 0 0 0 0.0087298 deletion chr10:9590601-9598000 7400 0 193986 1.51989e-13 265833 1.59372e-07 0 duplication chr10:9598001-20649900 1.10519e+07 3.11348e+07 0 0 0 0 0.0164661 deletion chr10:20649901-20666600 16700 2.04526e+07 0.107276 1.53471e-41 1.16667 1.60926e-35 0.0105263 duplication chr10:20666601-58953000 3.82864e+07 2.68946e+07 0 0 0 0 0.0687549 deletion chr10:58956801-58966800 10000 0 143550 2.26481e-21 179437 2.37483e-15 0 deletion chr10:58967101-58971500 4400 0 326250 0.000163197 598125 171.125 1 duplication chr10:58971501-67192000 8.2205e+06 2.50849e+07 0 0 0 0 0.00724827
过滤后
CNV_type coordinates CNV_size normalized_RD p-val1 p-val2 p-val3 p-val4 q0 deletion chr6:17969101-17990800 21700 0.0938754 7.34436e-12 1.50881e+09 1.0517e-10 1.60098e+09 0 deletion chr6:51409801-51432200 22400 0.130833 1.36433e-05 2.85248e+09 0.00071419 2.85413e+09 0.2 deletion chr6:62722501-62745900 23400 0.155307 0.00782878 2.87083e+09 54829.5 7.85916e-67 0 deletion chr6:63945701-63964200 18500 0.158415 0.0224522 2.8557e+09 0.60604 2.85735e+09 0.5 deletion chr6:84412301-84430800 18500 0.158415 0.0224522 2.8557e+09 0.60604 2.85735e+09 0.5 deletion chr6:94104601-94138600 34000 0.11393 3.51557e-09 2.87096e+09 34881.6 2.93187e-104 0 deletion chr6:95677601-95830900 153300 0.175024 2.02724e-10 2.871e+09 1.05335e-12 2.871e+09 0 deletion chr6:101751601-101764300 12700 0.157061 0.0380917 1.82699e+09 3.6824 1.96178e+09 0.5 deletion chr6:128498001-128514200 16200 0.138074 0.000294307 2.36381e+09 86017.5 2.08126e-41 0 deletion chr6:157641201-157696200 55000 0.132152 2.99676e-06 2.871e+09 19396 2.07431e-178 0 deletion chr6:167942101-168043600 101500 0.0540112 1.57017e-12 2.871e+09 8919.17 0 0 deletion chr6:171052901-171115100 62200 0.150971 0.000636157 2.871e+09 16651.8 7.83291e-204 0.333333 deletion chrM:8801-16600 7800 0.590908 2.54587e-08 2.42617e+09 0.000434635 2.53319e+09 0.00227964
过滤脚本
#!/usr/bin/perl -w use strict; die "Usage:\n\tperl filterCNV.pl <CNVs> \n" unless @ARGV == 1; my $cnv = shift; open CNV,"<$cnv" || die "$!"; my @pl = ""; while(<CNV>) { chomp; if ($_ =~ /normalized_RD/) { print "$_\n"; next; } @pl = split /\t/,$_; if($pl[3] ==0 || $pl[3] >4 ||$pl[8] == -1 || $pl[8] > 0.5 || $pl[2] < 1000) { next; }else { print $_ . "\n"; } } close CNV;
结语:
CNV的可靠性不高,一般人可以检测出1k~2k个,没有较好的验证方法(exome SNP还可以用芯片来评估)
所以建议多用几个软件来call CNV,另外可以设置上面的q0 参数,到0.1,甚至0.05(上面脚本中的pl[8])
版权声明:本文为leezx原创文章,遵循 CC 4.0 BY-SA 版权协议,转载请附上原文出处链接和本声明。