Remove VCF header lines
5
7
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12.0 years ago
win ▴ 990

Hi all,

Is there a simple way to remove header lines from a vcf file.

Although I would like to retain the "original" VCF file as well. So ideally if results.vcf is my file then I want to create results-noheader.vcf as another file without the header lines.

Any way this can be done?

Thanks in advance.

vcf • 22k views
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15
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12.0 years ago

Using negative matching:

-v, --invert-match select non-matching lines

egrep -v "^#" original.vcf > no_header.vcf
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7
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12.0 years ago
Wen.Huang ★ 1.2k

Using sed

sed '/^#/d' your.vcf > noheader.vcf
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3
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12.0 years ago
Vivek ★ 2.7k

Using awk:

awk '! /\#/' variants.VCF > no_header.VCF
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3
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4.0 years ago
hackdna ▴ 30

Using bcftools (https://www.htslib.org/doc/bcftools.html#view):

bcftools view --no-header results.vcf > results-noheader.vcf
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0
Entering edit mode
12.0 years ago

Perl version:

#!/usr/bin/perl
use strict; 
use warnings;
# no_headers.pl
# Reads a vcf file and removes unwanted headers
my $file = shift;
open my $F, $file;
LINE: while ($_=<$F>) {
next if /^##/; # This removes your headers
my @line = split /\t/;
print join(qq/\t/,@line);
}

Then you can do:

$ perl no_headers.pl your.vcf > no_headers.vcf

Of course, the one liner already submitted is quicker & better.

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2
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perl -lane 'print unless (m/^#/)' < file.vcf > noheader.vcf
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0
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Oh sure...everyone wants one-liners... ;)

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0
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easy to apply and easy to forget ...

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