I'm trying to merge some rather large VCF files using the joinx1.8 vcf-merge tool. The problem is that before the merging has finished, I receive a segmentation fault error. It seems that > 90% of the input files are successfully merged before the error occurs. I've repeated the command using joinx1.6 and 1.7, but they too produce a segmentation fault.
I am running Linux Mint 16 64-bit and I installed joinx using the "sudo apt-get install joinx1.8" command, after adding the requisite repository, and after installing the prerequisite libraries as per the joinx website.
I realize that vcftools also has a merging tool, but I have found that the joinx version is much faster.
The command I am using is:
"joinx1.8 vcf-merge -i first_file.vcf second_file.vcf -o merged_file.vcf &"
Any help would be much appreciated.