#63 vcf-merge missing SNPs in merge

[Anna Nash]

Hi,

I have an issue with vcf-merge: when merging 20 vcfs, I'm noticing that vcf-merge is creating a merged vcf but is missing out large chunks of SNPs from files (around 20k SNPs), but only on two chromosomes. This is using vcftools v.0.1.11. I appreciate this isn't the most up-to-date version, but it's the only version of the shared computing system in my department. If you think this would be easily resolved by an update to the latest version of vcftool I will contact the system administrator to update. Otherwise, any suggestions as to how to resolve this would be greatly appreciated.

Thanks