Joinx Vcf-Merge Produces A Segmentation Fault Before Merging Is Complete

Question

[jonorman]

Hi all,

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.

Thanks Joe

Answer 1

[jonorman]

Hi all,

I figured out the problem. The VCF files must be sorted by "joinx sort" beforehand. I had previously sorted the VCF files during other preprocessing steps, but it seems that all sorters are not created equal.

Joe