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.
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