How to combine chromosome vcf files

Question

[williamsbrian5064]

Hi,

Easy question here. I am split up my vcf file up by chromosome to try and save some time. I want to combine the files now to have one complete vcf file with all the chromosomes. Do I wanted to merge the files or do I want to concatenate the files?

I just ran the command

cat *.vcf > cat.chr1.chr2.vcf

This was only on two of the chromosomes and when I went to look at the files, there was only data for the first chromosome and nothing for the second. Am I doing something wrong here? I could also try vcf tools if this "cat" command wont work for what I am trying to do.

Answer 1

[Pierre Lindenbaum]

first alternative, use one vcf file to get the header, and the concatenante all the other vcf without the header (this was your error)

grep '^#' chr1.vcf > merge.vcf
grep -v '^#' chr1.vcf  chr2.vcf chr3.vcf chr4.vcf   >> merge.vcf

second alternative: use picard gatherVcfs http://broadinstitute.github.io/picard/command-line-overview.html, which is going to check the headers, orders etc...

java -jar picard.jar GatherVcfs I=chr1.vcf  I=chr2.vcf I=chr3.vcf I=chr4.vcf  O=merged.vcf

update 2023:

use bcftools concat

[williamsbrian5064]

Wonderful Pierre! Worked like a charm! Thank you so much for the help!

[mab658]

Hi Pierre, I wanted to merge VCF files which had already splitted by chromosones into a single file. Though each is compressed i.e. chr1.vcf.gz, chr2.vcf.gz, ......chrn.vcf.gz.

I could not see any an output file merged.vcf.gz when I used the command. Is it because the file is compressed?

java -jar /programs/picard-tools-2.18.11/picard.jar GatherVcfs I=chr1.vcf.gz I=chr2.vcf.gz O=merged.vcf.gz

[Jautis]

Hi Pierre, do you know if it's possible to use GatherVCFs with a list of files rather than a separate I= for each? Thanks!

[Pierre Lindenbaum]

try to use a text file WITH THE SUFFIX .list containing the path to the files.