how to merge sets of multi-vcf files

Question

[Ahmed Alhendi]

Hi,

I am trying to merge ~ 10,000 of vcf files into one vcf file, and I run to bcftools merge but it failed (segmentation fault) due to the large number of vcf files which I guess it is a software limitation. Then I tried to do so as batchs of 2000 vcf files at a time, which just worked fine, results in five sets of multi-vcf files (2000 samples each).

The question is how can I combine these multi-vcf files into one large multi-vcf file?

Any advice and suggestions will be greatly appreciated.

Answer 1

[Ram]

After this batch operation, you have 5 files with 2000 samples each, correct? Have you tried using bcftools merge on these 5 files? Maybe the limitation was on the number of files, not on the number of samples.

[Ahmed Alhendi]

Thanks for your quick reply. It actually works!

[Ram]

You're welcome. Please click on the green check mark to accept my answer and mark your question as resolved.