Breaking PLINK.bim .bed .fam files into chromosomes
3
2
Entering edit mode
21 months ago
safiradrak ▴ 20

Hello,

I am trying to get haplotypes for one locus on chromosome19 and for that, I need phased data. However, prior to the phasing, I am supposed to split my PLINK files into separated files by chromosome. I found this script online but it doesn't work (see below). Can you please give me advice on how to do this? I am rather a newbie in the data processing so I am sorry if this is a too basic question.

Thank you!

#!/usr/bin/perl

# This script takes as input the base filename of binary pedfiles (*.bed, 
# *.bim, *.fam) and a base output filename and splits up a dataset by 
# chromosome. Useful for imputing to 1000 genomes. 

chomp(my $pwd = `pwd`); my $help = "\nUsage: $0 <BEDfile base> <output base>\n\n"; die $help if @ARGV!=2;

$infile_base=$ARGV[0]; #base filename of inputs $outfile_base=$ARGV[1]; #base filename of outputs $plink_exec="plink
--nonfounders --allow-no-sex --noweb"; $chr=22; #last chromosome to write out


for (1..$chr) {     print "Processing chromosome $_\n";     `$plink_exec
--bfile $infile_base --chr $_ --make-bed --out ${outfile_base}$_;` }
SNP plink • 2.9k views
ADD COMMENT
4
Entering edit mode
21 months ago
zx8754 10k

No need for scripts, simple loop should work, something like:

for chr in {1..23}; do \
plink --bfile myPlink --chr $chr --make-bed --out myPlink_${chr}; \
done
ADD COMMENT
1
Entering edit mode
21 months ago
AK ★ 2.0k

I think the correct format is (in case some codes are commented out):

#!/usr/bin/perl

# This script takes as input the base filename of binary pedfiles (*.bed,
# *.bim, *.fam) and a base output filename and splits up a dataset by
# chromosome. Useful for imputing to 1000 genomes.

chomp( my $pwd = `pwd` );
my $help = "\nUsage: $0 <BEDfile base> <output base>\n\n";
die $help if @ARGV != 2;

$infile_base  = $ARGV[0];    #base filename of inputs
$outfile_base = $ARGV[1];    #base filename of outputs
$plink_exec = "plink --nonfounders --allow-no-sex --noweb";
$chr = 22;                   #last chromosome to write out

for ( 1 .. $chr ) {
    print "Processing chromosome $_\n";
    `$plink_exec --bfile $infile_base --chr $_ --make-bed --out ${outfile_base}$_;`;
}
ADD COMMENT

Login before adding your answer.

Traffic: 1455 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6