-
Notifications
You must be signed in to change notification settings - Fork 18
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
11 changed files
with
93 additions
and
41 deletions.
There are no files selected for viewing
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| #!/usr/bin/perl | ||
| use strict; | ||
| use warnings; | ||
| use 5.010; | ||
| local $SIG{__WARN__} = sub {my $message =shift; die $message;}; | ||
|
|
||
| # Author: Rajesh Patidar rajbtpatidar@gmail.com | ||
| # This scripts take 4 inputs (in the order listed) | ||
| # 1 a list of variants (chr\tstart\tend\ref\talt\totherInfo) which should be filtered out from the | ||
| # 2 a bed file of regions to be excluded from filtering out | ||
| # 3 file to work on, must be annotated using khanlab annotation-pipeline/ngs-pipeline | ||
| # 4 MAF filter (0.05) This remove any variant if present in any manoj/minor 1000g/ES/ExAC population. | ||
| # | ||
| # | ||
| open(BLACK, $ARGV[0]); | ||
| open(WHITE, $ARGV[1]); | ||
| open(IN, $ARGV[2]); | ||
| my $freq = $ARGV[3]; | ||
| my %REMOVE; | ||
| while(<BLACK>){ | ||
| chomp; | ||
| my @t =split("\t", $_); | ||
| $REMOVE{"$t[0]\t$t[1]\t$t[2]\t$t[3]\t$t[4]"} ="$t[5]"; | ||
| } | ||
| close BLACK; | ||
| my %KEEP; | ||
| while(<WHITE>){ | ||
| chomp; | ||
| my @t =split("\t", $_); | ||
| $KEEP{"$t[0]\t$t[1]\t$t[2]"} ="$t[3]"; | ||
| } | ||
| while(<IN>){ | ||
| chomp; | ||
| if($_ =~ /^Chr/){ | ||
| print "$_\n"; | ||
| next; | ||
| } | ||
| my @a = split ("\t", $_); | ||
| if (exists $REMOVE{"$a[0]\t$a[1]\t$a[2]\t$a[3]\t$a[4]"}){ | ||
| next; | ||
| } | ||
| foreach my $key (keys %KEEP){ | ||
| my @region= split("\t", $key); | ||
| if($a[0] =~ /^$region[0]$/ and $a[1] >=$region[1] and $a[1] <= $region[2]){ | ||
| print "$_\n"; | ||
| next; | ||
| } | ||
| } | ||
| #if(exists $KEEP{"$a[0]\t$a[1]\t$a[2]\t$a[3]\t$a[4]"}){ | ||
| # print "$_\n"; | ||
| # next; | ||
| #} | ||
| if($a[5] =~ /^exonic/ and ($a[8] =~ /nonsynonymous/ or $a[8] =~ /stop/ or $a[8] =~ /frameshift/) or $a[5] =~ /^splicing/){ | ||
| for (@a[12..28]){ | ||
| s/^\.$/-2/; | ||
| } | ||
| if( $a[12] <=$freq and $a[13] <=$freq and $a[14] <=$freq and $a[15] <=$freq and $a[16] <=$freq and $a[17] <=$freq and $a[18] <=$freq and $a[19] <=$freq and $a[20] <=$freq and $a[21] <=$freq and $a[22] <=$freq and $a[23] <=$freq and $a[24] <=$freq and $a[25] <=$freq and $a[26] <=$freq and $a[27] <=$freq and $a[28] <=$freq){ | ||
| print "$_\n"; | ||
| } | ||
| } | ||
| } | ||
| close IN; |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters