File: vcfOnlyAlts.pl

package info (click to toggle)
snpeff 5.4.b%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid
  • size: 757,496 kB
  • sloc: java: 62,572; perl: 2,279; sh: 1,185; python: 744; xml: 507; makefile: 50
file content (14 lines) | stat: -rwxr-xr-x 241 bytes parent folder | download | duplicates (3) 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
 
#!/usr/bin/perl

while( $l = <STDIN> ) {

	if( $l =~ /^#/ ) { 
		print $l; 
	} else {
		@t = split /\t/, $l;
		$alt = $t[4];

		# Show if ALT fiels is not empty and doesn't have '<'
		if(( $alt ne '.' ) && ($alt !~ /^</)) { print $l; }
	}
}