I have 280 vcf files, each containing about 200 SNPs from a genotyping experiment. I need to merge all these so I can have a final combined vcf where I have all SNPs in all individuals, that is if an individual lacks that SNP, in the combined file it is coded as ./. or .
I am using the following command from vcftools: vcf-merge A.vcf.gz B.vcf.gz C.vcf.gz | bgzip -c > out.vcf.gz
It worked for two files, although it took about 1 hour, now it's been running of 1 day for the whole 280 files. I was wondering if this is the only way of merging a large number of vcf files or if there is any other way to make it more efficient?